def __init__(self, parent=None, logname=None, level=logging.NOTSET):
QWidget.__init__(self, parent=parent)
# Create Widgets
self.label = QLabel('Minimum displayed log level: ', parent=self)
self.combo = QComboBox(parent=self)
self.text = QPlainTextEdit(parent=self)
self.text.setReadOnly(True)
self.clear_btn = QPushButton("Clear", parent=self)
# Create layout
layout = QVBoxLayout()
level_control = QHBoxLayout()
level_control.addWidget(self.label)
level_control.addWidget(self.combo)
layout.addLayout(level_control)
layout.addWidget(self.text)
layout.addWidget(self.clear_btn)
self.setLayout(layout)
# Allow QCombobox to control log level
for log_level, value in LogLevels.as_dict().items():
self.combo.addItem(log_level, value)
self.combo.currentIndexChanged[str].connect(self.setLevel)
# Allow QPushButton to clear log text
self.clear_btn.clicked.connect(self.clear)
# Create a handler with the default format
self.handler = GuiHandler(level=level, parent=self)
self.logFormat = self.default_format
self.handler.message.connect(self.write)
# Create logger. Either as a root or given logname
self.log = None
self.level = None
self.logName = logname or ''
self.logLevel = level
self.destroyed.connect(functools.partial(logger_destroyed, self.log))
def __init__(self, parent=None):
QPlainTextEdit.__init__(self, parent)
BaseEditMixin.__init__(self)
self.setAttribute(Qt.WA_DeleteOnClose)
self.extra_selections_dict = {}
self.textChanged.connect(self.changed)
self.cursorPositionChanged.connect(self.cursor_position_changed)
self.indent_chars = " "*4
self.tab_stop_width_spaces = 4
# Code completion / calltips
if parent is not None:
mainwin = parent
while not isinstance(mainwin, QMainWindow):
mainwin = mainwin.parent()
if mainwin is None:
break
if mainwin is not None:
parent = mainwin
self.completion_widget = CompletionWidget(self, parent)
self.codecompletion_auto = False
self.setup_completion()
self.calltip_widget = CallTipWidget(self, hide_timer_on=False)
self.calltip_position = None
self.tooltip_widget = ToolTipWidget(parent, as_tooltip=True)
self.has_cell_separators = False
self.highlight_current_cell_enabled = False
# The color values may be overridden by the syntax highlighter
# Highlight current line color
self.currentline_color = QColor(Qt.red).lighter(190)
self.currentcell_color = QColor(Qt.red).lighter(194)
# Brace matching
self.bracepos = None
self.matched_p_color = QColor(Qt.green)
self.unmatched_p_color = QColor(Qt.red)
self.last_cursor_cell = None
self.decorations = TextDecorationsManager(self)
def wheelEvent(self, event):
"""Reimplemented to emit zoom in/out signals when Ctrl is pressed"""
# This feature is disabled on MacOS, see Issue 1510
if sys.platform != 'darwin':
if event.modifiers() & Qt.ControlModifier:
if hasattr(event, 'angleDelta'):
if event.angleDelta().y() < 0:
self.zoom_out.emit()
elif event.angleDelta().y() > 0:
self.zoom_in.emit()
elif hasattr(event, 'delta'):
if event.delta() < 0:
self.zoom_out.emit()
elif event.delta() > 0:
self.zoom_in.emit()
return
QPlainTextEdit.wheelEvent(self, event)
self.highlight_current_cell()
class DisplayDialog(QDialog):
"""
This is a simple dialog display which can be configured by users
"""
def __init__(self, parent=None, name='Test'):
""" init
:param parent:
"""
super(DisplayDialog, self).__init__(parent)
layout = QVBoxLayout(self)
# nice widget for editing the date
self.message_edit = QPlainTextEdit(self)
self.message_edit.setReadOnly(True)
layout.addWidget(self.message_edit)
self.setWindowTitle('Merged Scans Workspace Names')
# OK and Cancel buttons
buttons = QDialogButtonBox(QDialogButtonBox.Ok, QtCore.Qt.Horizontal, self)
buttons.accepted.connect(self.accept)
layout.addWidget(buttons)
self.name = name
return
def set_name(self, new_name):
self.name = new_name
def show_message(self, message):
"""
show message
:param message:
:return:
"""
self.message_edit.setPlainText(message)
return
class OutputPreviewWidget(QWidget):
"""
A .py preview widget that appears as a drawer on the side of the main
import widget.
"""
def __init__(self, parent=None):
super(OutputPreviewWidget, self).__init__(parent=parent)
self.setWindowFlags(Qt.Sheet)
self.text_editor = QPlainTextEdit()
self.close_button = QPushButton('Close')
self.layout = QVBoxLayout()
self.layout.addWidget(self.text_editor)
self.layout.addWidget(self.close_button)
self.setLayout(self.layout)
self.close_button.clicked.connect(self.hide)
self.resize(400, 500)
font = QFont('Courier')
self.text_editor.setFont(font)
self.text_editor.setReadOnly(True)
def set_text(self, text):
"""
Set the text in the loader preview widget. This will display the text that
will be saved to the output loader python file.
Parameters
----------
text: str
Text that will be saved to the final loader file
"""
self.text_editor.setPlainText(text)
def __init__(self, parent=None):
super(OutputPreviewWidget, self).__init__(parent=parent)
self.setWindowFlags(Qt.Sheet)
self.text_editor = QPlainTextEdit()
self.close_button = QPushButton('Close')
self.layout = QVBoxLayout()
self.layout.addWidget(self.text_editor)
self.layout.addWidget(self.close_button)
self.setLayout(self.layout)
self.close_button.clicked.connect(self.hide)
self.resize(400, 500)
font = QFont('Courier')
self.text_editor.setFont(font)
self.text_editor.setReadOnly(True)
def __init__(self, parent=None, label_name=''):
"""
:param parent:
:param label_name
"""
super(GetValueDialog, self).__init__(parent)
layout = QVBoxLayout(self)
# details information
self.info_line = QPlainTextEdit(self)
self.info_line.setEnabled(False)
layout.addWidget(self.info_line)
# input
self.label = QLabel(self)
self.value_edit = QLineEdit(self)
layout.addWidget(self.label)
layout.addWidget(self.value_edit)
# END-IF-ELSE
# nice widget for editing the date
# self.datetime = QDateTimeEdit(self)
# self.datetime.setCalendarPopup(True)
# self.datetime.setDateTime(QDateTime.currentDateTime())
# layout.addWidget(self.datetime)
# OK and Cancel buttons
buttons = QDialogButtonBox(QDialogButtonBox.Ok | QDialogButtonBox.Cancel,
QtCore.Qt.Horizontal, self)
buttons.accepted.connect(self.accept)
buttons.rejected.connect(self.reject)
layout.addWidget(buttons)
# set some values
self.setWindowTitle('Get user input')
self.label.setText(label_name)
return
def create_textedit(self, text, option, default=NoDefault,
tip=None, restart=False):
label = QLabel(text)
label.setWordWrap(True)
edit = QPlainTextEdit()
edit.setWordWrapMode(QTextOption.WordWrap)
layout = QVBoxLayout()
layout.addWidget(label)
layout.addWidget(edit)
layout.setContentsMargins(0, 0, 0, 0)
if tip:
edit.setToolTip(tip)
self.textedits[edit] = (option, default)
widget = QWidget(self)
widget.label = label
widget.textbox = edit
widget.setLayout(layout)
edit.restart_required = restart
edit.label_text = text
return widget
def __init__(self, parent=None, name='Test'):
""" init
:param parent:
"""
super(DisplayDialog, self).__init__(parent)
layout = QVBoxLayout(self)
# nice widget for editing the date
self.message_edit = QPlainTextEdit(self)
self.message_edit.setReadOnly(True)
layout.addWidget(self.message_edit)
self.setWindowTitle('Merged Scans Workspace Names')
# OK and Cancel buttons
buttons = QDialogButtonBox(QDialogButtonBox.Ok, QtCore.Qt.Horizontal, self)
buttons.accepted.connect(self.accept)
layout.addWidget(buttons)
self.name = name
return
def mousePressEvent(self, event):
"""Reimplement Qt method"""
if sys.platform.startswith('linux') and event.button() == Qt.MidButton:
self.calltip_widget.hide()
self.setFocus()
event = QMouseEvent(QEvent.MouseButtonPress, event.pos(),
Qt.LeftButton, Qt.LeftButton, Qt.NoModifier)
QPlainTextEdit.mousePressEvent(self, event)
QPlainTextEdit.mouseReleaseEvent(self, event)
# Send selection text to clipboard to be able to use
# the paste method and avoid the strange Issue 1445
# NOTE: This issue seems a focusing problem but it
# seems really hard to track
mode_clip = QClipboard.Clipboard
mode_sel = QClipboard.Selection
text_clip = QApplication.clipboard().text(mode=mode_clip)
text_sel = QApplication.clipboard().text(mode=mode_sel)
QApplication.clipboard().setText(text_sel, mode=mode_clip)
self.paste()
QApplication.clipboard().setText(text_clip, mode=mode_clip)
else:
self.calltip_widget.hide()
QPlainTextEdit.mousePressEvent(self, event)
def focusInEvent(self, event):
"""Reimplemented to handle focus"""
self.focus_changed.emit()
self.focus_in.emit()
self.highlight_current_cell()
QPlainTextEdit.focusInEvent(self, event)
def focusOutEvent(self, event):
"""Reimplemented to handle focus"""
self.focus_changed.emit()
QPlainTextEdit.focusOutEvent(self, event)
def __init__(self, settings: PartSettings):
super().__init__()
self._settings = settings
self.export_btn = QPushButton("Export profile")
self.export_btn.clicked.connect(self.export_profile)
self.import_btn = QPushButton("Import profile")
self.import_btn.clicked.connect(self.import_profiles)
self.export_pipeline_btn = QPushButton("Export pipeline")
self.export_pipeline_btn.clicked.connect(self.export_pipeline)
self.import_pipeline_btn = QPushButton("Import pipeline")
self.import_pipeline_btn.clicked.connect(self.import_pipeline)
self.delete_btn = QPushButton("Delete profile")
self.delete_btn.setDisabled(True)
self.delete_btn.clicked.connect(self.delete_profile)
self.multiple_files_chk = QCheckBox("Show multiple files panel")
self.multiple_files_chk.setChecked(
self._settings.get("multiple_files_widget", False))
self.multiple_files_chk.stateChanged.connect(
self.multiple_files_visibility)
self.rename_btn = QPushButton("Rename profile")
self.rename_btn.clicked.connect(self.rename_profile)
self.rename_btn.setDisabled(True)
self.voxel_size_label = QLabel()
self.info_label = QPlainTextEdit()
self.info_label.setReadOnly(True)
self.profile_list = SearchableListWidget()
self.profile_list.currentTextChanged.connect(self.profile_chosen)
self.pipeline_list = SearchableListWidget()
self.pipeline_list.currentTextChanged.connect(self.profile_chosen)
self.spacing = [QDoubleSpinBox() for _ in range(3)]
self.lock_spacing = LockCheckBox()
self.lock_spacing.stateChanged.connect(self.spacing[1].setDisabled)
self.lock_spacing.stateChanged.connect(self.synchronize_spacing)
# noinspection PyUnresolvedReferences
self.spacing[2].valueChanged.connect(self.synchronize_spacing)
units_value = self._settings.get("units_value", Units.nm)
for el in self.spacing:
el.setAlignment(Qt.AlignRight)
el.setButtonSymbols(QAbstractSpinBox.NoButtons)
el.setRange(0, 1000000)
# noinspection PyUnresolvedReferences
el.valueChanged.connect(self.image_spacing_change)
self.units = EnumComboBox(Units)
self.units.set_value(units_value)
# noinspection PyUnresolvedReferences
self.units.currentIndexChanged.connect(self.update_spacing)
spacing_layout = QHBoxLayout()
spacing_layout.addWidget(self.lock_spacing)
for txt, el in zip(["x", "y", "z"], self.spacing[::-1]):
spacing_layout.addWidget(QLabel(txt + ":"))
spacing_layout.addWidget(el)
spacing_layout.addWidget(self.units)
spacing_layout.addStretch(1)
voxel_size_layout = QHBoxLayout()
voxel_size_layout.addWidget(self.voxel_size_label)
voxel_size_layout.addSpacing(30)
profile_layout = QGridLayout()
profile_layout.setSpacing(0)
profile_layout.addWidget(QLabel("Profiles:"), 0, 0)
profile_layout.addWidget(self.profile_list, 1, 0)
profile_layout.addWidget(QLabel("Pipelines:"), 2, 0)
profile_layout.addWidget(self.pipeline_list, 3, 0, 4, 1)
profile_layout.addWidget(self.info_label, 1, 1, 3, 2)
profile_layout.addWidget(self.export_btn, 4, 1)
profile_layout.addWidget(self.import_btn, 4, 2)
profile_layout.addWidget(self.export_pipeline_btn, 5, 1)
profile_layout.addWidget(self.import_pipeline_btn, 5, 2)
profile_layout.addWidget(self.delete_btn, 6, 1)
profile_layout.addWidget(self.rename_btn, 6, 2)
layout = QVBoxLayout()
layout.addLayout(spacing_layout)
layout.addLayout(voxel_size_layout)
layout.addWidget(self.multiple_files_chk)
layout.addLayout(profile_layout, 1)
self.setLayout(layout)
class PyDMLogDisplay(QWidget, LogLevels):
"""
Standard display for Log Output
This widget handles instantating a ``GuiHandler`` and displaying log
messages to a ``QPlainTextEdit``. The level of the log can be changed from
inside the widget itself, allowing users to select from any of the
``.levels`` specified by the widget.
Parameters
----------
parent : QObject, optional
logname : str
Name of log to display in widget
level : logging.Level
Initial level of log display
"""
Q_ENUMS(LogLevels)
LogLevels = LogLevels
terminator = '\n'
default_format = '%(asctime)s %(message)s'
default_level = logging.INFO
def __init__(self, parent=None, logname=None, level=logging.NOTSET):
QWidget.__init__(self, parent=parent)
# Create Widgets
self.label = QLabel('Minimum displayed log level: ', parent=self)
self.combo = QComboBox(parent=self)
self.text = QPlainTextEdit(parent=self)
self.text.setReadOnly(True)
self.clear_btn = QPushButton("Clear", parent=self)
# Create layout
layout = QVBoxLayout()
level_control = QHBoxLayout()
level_control.addWidget(self.label)
level_control.addWidget(self.combo)
layout.addLayout(level_control)
layout.addWidget(self.text)
layout.addWidget(self.clear_btn)
self.setLayout(layout)
# Allow QCombobox to control log level
for log_level, value in LogLevels.as_dict().items():
self.combo.addItem(log_level, value)
self.combo.currentIndexChanged[str].connect(self.setLevel)
# Allow QPushButton to clear log text
self.clear_btn.clicked.connect(self.clear)
# Create a handler with the default format
self.handler = GuiHandler(level=level, parent=self)
self.logFormat = self.default_format
self.handler.message.connect(self.write)
# Create logger. Either as a root or given logname
self.log = None
self.level = None
self.logName = logname or ''
self.logLevel = level
def sizeHint(self):
return QSize(400, 300)
@Property(LogLevels)
def logLevel(self):
return self.level
@logLevel.setter
def logLevel(self, level):
if level != self.level:
self.level = level
idx = self.combo.findData(level)
self.combo.setCurrentIndex(idx)
@Property(str)
def logName(self):
"""Name of associated log"""
return self.log.name
@logName.setter
def logName(self, name):
# Disconnect prior log from handler
if self.log:
self.log.removeHandler(self.handler)
# Reattach handler to new handler
self.log = logging.getLogger(name)
# Ensure that the log matches level of handler
# only if the handler level is less than the log.
if self.log.level < self.handler.level:
self.log.setLevel(self.handler.level)
# Attach preconfigured handler
self.log.addHandler(self.handler)
@Property(str)
def logFormat(self):
"""Format for log messages"""
return self.handler.formatter._fmt
@logFormat.setter
def logFormat(self, fmt):
self.handler.setFormatter(logging.Formatter(fmt))
@Slot(str)
def write(self, message):
"""Write a message to the log display"""
# We split the incoming message by new lines. In prior iterations of
# this widget it was discovered that large blocks of text cause issues
# at the Qt level.
for msg in message.split(self.terminator):
self.text.appendPlainText(msg)
@Slot()
def clear(self):
"""Clear the text area."""
self.text.clear()
@Slot(str)
def setLevel(self, level):
"""Set the level of the contained logger"""
# Get the level from the incoming string specification
try:
level = getattr(logging, level.upper())
except AttributeError as exc:
logger.exception("Invalid logging level specified %s",
level.upper())
else:
# Set the existing handler and logger to this level
self.handler.setLevel(level)
if self.log.level > self.handler.level or self.log.level == logging.NOTSET:
self.log.setLevel(self.handler.level)
class MOSVizViewer(DataViewer):
LABEL = "MOSViz Viewer"
window_closed = Signal()
_toolbar_cls = MOSViewerToolbar
tools = []
subtools = []
def __init__(self, session, parent=None):
super(MOSVizViewer, self).__init__(session, parent=parent)
self.slit_controller = SlitController(self)
self.load_ui()
# Define some data containers
self.filepath = None
self.savepath = None
self.data_idx = None
self.comments = False
self.textChangedAt = None
self.mask = None
self.cutout_wcs = None
self.level2_data = None
self.spec2d_data = None
self.catalog = None
self.current_row = None
self._specviz_instance = None
self._loaded_data = {}
self._primary_data = None
self._layer_view = SimpleLayerWidget(parent=self)
self._layer_view.layer_combo.currentIndexChanged.connect(self._selection_changed)
self.resize(800, 600)
self.image_viewer_hidden = False
def load_ui(self):
"""
Setup the MOSView viewer interface.
"""
self.central_widget = QWidget(self)
path = os.path.join(UI_DIR, 'mos_widget.ui')
loadUi(path, self.central_widget)
self.image_widget = DrawableImageWidget(slit_controller=self.slit_controller)
self.spectrum2d_widget = Spectrum2DWidget()
self._specviz_viewer = Workspace()
self._specviz_viewer.add_plot_window()
self.spectrum1d_widget = self._specviz_viewer.current_plot_window
self.spectrum1d_widget.plot_widget.getPlotItem().layout.setContentsMargins(45, 0, 25, 0)
# Set up helper for sharing axes. SharedAxisHelper defaults to no sharing
# and we control the sharing later by setting .sharex and .sharey on the
# helper
self.spectrum2d_image_share = SharedAxisHelper(self.spectrum2d_widget._axes,
self.image_widget._axes)
# We only need to set the image widget to keep the same aspect ratio
# since the two other viewers don't require square pixels, so the axes
# should not change shape.
self.image_widget._axes.set_adjustable('datalim')
self.meta_form_layout = self.central_widget.meta_form_layout
self.meta_form_layout.setFieldGrowthPolicy(self.meta_form_layout.ExpandingFieldsGrow)
self.central_widget.left_vertical_splitter.insertWidget(0, self.image_widget)
self.central_widget.right_vertical_splitter.addWidget(self.spectrum2d_widget)
self.central_widget.right_vertical_splitter.addWidget(self.spectrum1d_widget.widget())
# Set the splitter stretch factors
self.central_widget.left_vertical_splitter.setStretchFactor(0, 1)
self.central_widget.left_vertical_splitter.setStretchFactor(1, 8)
self.central_widget.right_vertical_splitter.setStretchFactor(0, 1)
self.central_widget.right_vertical_splitter.setStretchFactor(1, 2)
self.central_widget.horizontal_splitter.setStretchFactor(0, 1)
self.central_widget.horizontal_splitter.setStretchFactor(1, 2)
# Keep the left and right splitters in sync otherwise the axes don't line up
self.central_widget.left_vertical_splitter.splitterMoved.connect(self._left_splitter_moved)
self.central_widget.right_vertical_splitter.splitterMoved.connect(self._right_splitter_moved)
# Set the central widget
self.setCentralWidget(self.central_widget)
self.central_widget.show()
# Define the options widget
self._options_widget = OptionsWidget()
def show(self, *args, **kwargs):
super(MOSVizViewer, self).show(*args, **kwargs)
# Trigger a sync between the splitters
self._left_splitter_moved()
if self.image_viewer_hidden:
self.image_widget.hide()
else:
self.image_widget.show()
@avoid_circular
def _right_splitter_moved(self, *args, **kwargs):
if self.image_widget.isHidden():
return
sizes = self.central_widget.right_vertical_splitter.sizes()
if sizes == [0, 0]:
sizes = [230, 230]
self.central_widget.left_vertical_splitter.setSizes(sizes)
@avoid_circular
def _left_splitter_moved(self, *args, **kwargs):
if self.image_widget.isHidden():
return
sizes = self.central_widget.left_vertical_splitter.sizes()
if sizes == [0, 0]:
sizes = [230, 230]
self.central_widget.right_vertical_splitter.setSizes(sizes)
def setup_connections(self):
"""
Connects gui elements to event calls.
"""
# Connect the selection event for the combo box to what's displayed
self.toolbar.source_select.currentIndexChanged[int].connect(
lambda ind: self.load_selection(self.catalog[ind]))
self.toolbar.source_select.currentIndexChanged[int].connect(
lambda ind: self._set_navigation(ind))
# Connect the exposure selection event
self.toolbar.exposure_select.currentIndexChanged[int].connect(
lambda ind: self.load_exposure(ind))
self.toolbar.exposure_select.currentIndexChanged[int].connect(
lambda ind: self._set_exposure_navigation(ind))
# Connect the specviz button
if SpecvizDataViewer is not None:
self.toolbar.open_specviz.triggered.connect(
lambda: self._open_in_specviz())
else:
self.toolbar.open_specviz.setDisabled(True)
# Connect slit previous and next buttons
self.toolbar.cycle_next_action.triggered.connect(
lambda: self._set_navigation(
self.toolbar.source_select.currentIndex() + 1))
self.toolbar.cycle_previous_action.triggered.connect(
lambda: self._set_navigation(
self.toolbar.source_select.currentIndex() - 1))
# Connect exposure previous and next buttons
self.toolbar.exposure_next_action.triggered.connect(
lambda: self._set_exposure_navigation(
self.toolbar.exposure_select.currentIndex() + 1))
self.toolbar.exposure_previous_action.triggered.connect(
lambda: self._set_exposure_navigation(
self.toolbar.exposure_select.currentIndex() - 1))
# Connect the toolbar axes setting actions
self.toolbar.lock_x_action.triggered.connect(
lambda state: self.set_locked_axes(x=state))
self.toolbar.lock_y_action.triggered.connect(
lambda state: self.set_locked_axes(y=state))
def options_widget(self):
return self._options_widget
def initialize_toolbar(self):
"""
Initialize the custom toolbar for the MOSViz viewer.
"""
from glue.config import viewer_tool
self.toolbar = self._toolbar_cls(self)
for tool_id in self.tools:
mode_cls = viewer_tool.members[tool_id]
mode = mode_cls(self)
self.toolbar.add_tool(mode)
self.addToolBar(self.toolbar)
self.setup_connections()
def register_to_hub(self, hub):
super(MOSVizViewer, self).register_to_hub(hub)
def has_data_or_subset(x):
if x.sender is self._primary_data:
return True
elif isinstance(x.sender, Subset) and x.sender.data is self._primary_data:
return True
else:
return False
hub.subscribe(self, msg.SubsetCreateMessage,
handler=self._add_subset,
filter=has_data_or_subset)
hub.subscribe(self, msg.SubsetUpdateMessage,
handler=self._update_subset,
filter=has_data_or_subset)
hub.subscribe(self, msg.SubsetDeleteMessage,
handler=self._remove_subset,
filter=has_data_or_subset)
hub.subscribe(self, msg.DataUpdateMessage,
handler=self._update_data,
filter=has_data_or_subset)
def add_data(self, data):
"""
Processes data message from the central communication hub.
Parameters
----------
data : :class:`glue.core.data.Data`
Data object.
"""
# Check whether the data is suitable for the MOSViz viewer - basically
# we expect a table of 1D columns with at least three string and four
# floating-point columns.
if data.ndim != 1:
QMessageBox.critical(self, "Error", "MOSViz viewer can only be used "
"for data with 1-dimensional components",
buttons=QMessageBox.Ok)
return False
components = [data.get_component(cid) for cid in data.main_components]
categorical = [c for c in components if c.categorical]
if len(categorical) < 3:
QMessageBox.critical(self, "Error", "MOSViz viewer expected at least "
"three string components/columns, representing "
"the filenames of the 1D and 2D spectra and "
"cutouts", buttons=QMessageBox.Ok)
return False
# We can relax the following requirement if we make the slit parameters
# optional
numerical = [c for c in components if c.numeric]
if len(numerical) < 4:
QMessageBox.critical(self, "Error", "MOSViz viewer expected at least "
"four numerical components/columns, representing "
"the slit position, length, and position angle",
buttons=QMessageBox.Ok)
return False
# Make sure the loaders and column names are correct
result = confirm_loaders_and_column_names(data)
if not result:
return False
self._primary_data = data
self._layer_view.data = data
self._unpack_selection(data)
return True
def add_data_for_testing(self, data):
"""
Processes data message from the central communication hub.
Parameters
----------
data : :class:`glue.core.data.Data`
Data object.
"""
# Check whether the data is suitable for the MOSViz viewer - basically
# we expect a table of 1D columns with at least three string and four
# floating-point columns.
if data.ndim != 1:
QMessageBox.critical(self, "Error", "MOSViz viewer can only be used "
"for data with 1-dimensional components",
buttons=QMessageBox.Ok)
return False
components = [data.get_component(cid) for cid in data.main_components]
categorical = [c for c in components if c.categorical]
if len(categorical) < 3:
QMessageBox.critical(self, "Error", "MOSViz viewer expected at least "
"three string components/columns, representing "
"the filenames of the 1D and 2D spectra and "
"cutouts", buttons=QMessageBox.Ok)
return False
# We can relax the following requirement if we make the slit parameters
# optional
numerical = [c for c in components if c.numeric]
if len(numerical) < 4:
QMessageBox.critical(self, "Error", "MOSViz viewer expected at least "
"four numerical components/columns, representing "
"the slit position, length, and position angle",
buttons=QMessageBox.Ok)
return False
# Block of code to bypass the loader_selection gui
#########################################################
if 'loaders' not in data.meta:
data.meta['loaders'] = {}
# Deimos data
data.meta['loaders']['spectrum1d'] = "DEIMOS 1D Spectrum"
data.meta['loaders']['spectrum2d'] = "DEIMOS 2D Spectrum"
data.meta['loaders']['cutout'] = "ACS Cutout Image"
if 'special_columns' not in data.meta:
data.meta['special_columns'] = {}
data.meta['special_columns']['spectrum1d'] = 'spectrum1d'
data.meta['special_columns']['spectrum2d'] = 'spectrum2d'
data.meta['special_columns']['source_id'] = 'id'
data.meta['special_columns']['cutout'] = 'cutout'
data.meta['special_columns']['slit_ra'] = 'ra'
data.meta['special_columns']['slit_dec'] = 'dec'
data.meta['special_columns']['slit_width'] = 'slit_width'
data.meta['special_columns']['slit_length'] = 'slit_length'
data.meta['loaders_confirmed'] = True
#########################################################
self._primary_data = data
self._layer_view.data = data
self._unpack_selection(data)
return True
def add_subset(self, subset):
"""
Processes subset messages from the central communication hub.
Parameters
----------
subset :
Subset object.
"""
self._layer_view.refresh()
index = self._layer_view.layer_combo.findData(subset)
self._layer_view.layer_combo.setCurrentIndex(index)
return True
def _update_data(self, message):
"""
Update data message.
Parameters
----------
message : :class:`glue.core.message.Message`
Data message object.
"""
self._layer_view.refresh()
def _add_subset(self, message):
"""
Add subset message.
Parameters
----------
message : :class:`glue.core.message.Message`
Subset message object.
"""
self._layer_view.refresh()
def _update_subset(self, message):
"""
Update subset message.
Parameters
----------
message : :class:`glue.core.message.Message`
Update message object.
"""
self._layer_view.refresh()
self._unpack_selection(message.subset)
def _remove_subset(self, message):
"""
Remove subset message.
Parameters
----------
message : :class:`glue.core.message.Message`
Subset message object.
"""
self._layer_view.refresh()
self._unpack_selection(message.subset.data)
def _selection_changed(self):
self._unpack_selection(self._layer_view.layer_combo.currentData())
def _unpack_selection(self, data):
"""
Interprets the :class:`glue.core.data.Data` object by decomposing the
data elements, extracting relevant data, and recomposing a
package-agnostic dictionary object containing the relevant data.
Parameters
----------
data : :class:`glue.core.data.Data`
Glue data object to decompose.
"""
mask = None
if isinstance(data, Subset):
try:
mask = data.to_mask()
except IncompatibleAttribute:
return
if not np.any(mask):
return
data = data.data
self.mask = mask
# Clear the table
self.catalog = Table()
self.catalog.meta = data.meta
self.comments = False
col_names = data.components
for att in col_names:
cid = data.id[att]
component = data.get_component(cid)
if component.categorical:
comp_labels = component.labels[mask]
if comp_labels.ndim > 1:
comp_labels = comp_labels[0]
if str(att) in ["comments", "flag"]:
self.comments = True
elif str(att) in ['level2', 'spectrum1d', 'spectrum2d', 'cutout']:
self.filepath = component._load_log.path
p = Path(self.filepath)
path = os.path.sep.join(p.parts[:-1])
self.catalog[str(att)] = [os.path.join(path, x)
for x in comp_labels]
else:
self.catalog[str(att)] = comp_labels
else:
comp_data = component.data[mask]
if comp_data.ndim > 1:
comp_data = comp_data[0]
self.catalog[str(att)] = comp_data
if len(self.catalog) > 0:
if not self.comments:
self.comments = self._load_comments(data.label) #Returns bool
else:
self._data_collection_index(data.label)
self._get_save_path()
# Update gui elements
self._update_navigation(select=0)
def _update_navigation(self, select=0):
"""
Updates the :class:`qtpy.QtWidgets.QComboBox` widget with the
appropriate source `id`s from the MOS catalog.
"""
if self.toolbar is None:
return
self.toolbar.source_select.blockSignals(True)
self.toolbar.source_select.clear()
if len(self.catalog) > 0 and self.catalog.meta["special_columns"]["source_id"] in self.catalog.colnames:
self.toolbar.source_select.addItems(self.catalog[self.catalog.meta["special_columns"]["source_id"]][:])
self.toolbar.source_select.setCurrentIndex(select)
self.toolbar.source_select.blockSignals(False)
self.toolbar.source_select.currentIndexChanged.emit(select)
def _set_navigation(self, index):
if len(self.catalog) < index:
return
if 0 <= index < self.toolbar.source_select.count():
self.toolbar.source_select.setCurrentIndex(index)
if index <= 0:
self.toolbar.cycle_previous_action.setDisabled(True)
else:
self.toolbar.cycle_previous_action.setDisabled(False)
if index >= self.toolbar.source_select.count() - 1:
self.toolbar.cycle_next_action.setDisabled(True)
else:
self.toolbar.cycle_next_action.setDisabled(False)
def _set_exposure_navigation(self, index):
# For level 3-only data.
if index == None:
# for some unknown reason (related to layout
# managers perhaps?), the combo box does not
# disappear from screen even when forced to
# hide. Next best solution is to disable it.
self.toolbar.exposure_select.setEnabled(False)
self.toolbar.exposure_next_action.setEnabled(False)
self.toolbar.exposure_previous_action.setEnabled(False)
return
if index > self.toolbar.exposure_select.count():
return
if 0 <= index < self.toolbar.exposure_select.count():
self.toolbar.exposure_select.setCurrentIndex(index)
if index < 1:
self.toolbar.exposure_previous_action.setEnabled(False)
else:
self.toolbar.exposure_previous_action.setEnabled(True)
if index >= self.toolbar.exposure_select.count() - 1:
self.toolbar.exposure_next_action.setEnabled(False)
else:
self.toolbar.exposure_next_action.setEnabled(True)
def _open_in_specviz(self):
if self._specviz_instance is None:
# Store a reference to the currently opened data viewer. This means
# new "open in specviz" events will be added to the current viewer
# as opposed to opening a new viewer.
self._specviz_instance = self.session.application.new_data_viewer(
SpecvizDataViewer)
# Clear the reference to ensure no qt dangling pointers
def _clear_instance_reference():
self._specviz_instance = None
self._specviz_instance.window_closed.connect(
_clear_instance_reference)
# Create a new Spectrum1D object from the flux data attribute of
# the incoming data
spec = glue_data_to_spectrum1d(self._loaded_data['spectrum1d'], 'Flux')
# Create a DataItem from the Spectrum1D object, which adds the data
# to the internel specviz model
data_item = self._specviz_instance.current_workspace.model.add_data(
spec, 'Spectrum1D')
self._specviz_instance.current_workspace.force_plot(data_item)
def load_selection(self, row):
"""
Processes a row in the MOS catalog by first loading the data set,
updating the stored data components, and then rendering the data on
the visible MOSViz viewer plots.
Parameters
----------
row : `astropy.table.Row`
A row object representing a row in the MOS catalog. Each key
should be a column name.
"""
self.current_row = row
# Get loaders
loader_spectrum1d = SPECTRUM1D_LOADERS[self.catalog.meta["loaders"]["spectrum1d"]]
loader_spectrum2d = SPECTRUM2D_LOADERS[self.catalog.meta["loaders"]["spectrum2d"]]
loader_cutout = CUTOUT_LOADERS[self.catalog.meta["loaders"]["cutout"]]
# Get column names
colname_spectrum1d = self.catalog.meta["special_columns"]["spectrum1d"]
colname_spectrum2d = self.catalog.meta["special_columns"]["spectrum2d"]
colname_cutout = self.catalog.meta["special_columns"]["cutout"]
level2_data = None
if "level2" in self.catalog.meta["loaders"]:
loader_level2 = LEVEL2_LOADERS[self.catalog.meta["loaders"]["level2"]]
colname_level2 = self.catalog.meta["special_columns"]["level2"]
level2_basename = os.path.basename(row[colname_level2])
if level2_basename != "None":
level2_data = loader_level2(row[colname_level2])
spec1d_basename = os.path.basename(row[colname_spectrum1d])
if spec1d_basename == "None":
spec1d_data = None
else:
spec1d_data = loader_spectrum1d(row[colname_spectrum1d])
spec2d_basename = os.path.basename(row[colname_spectrum2d])
if spec2d_basename == "None":
spec2d_data = None
else:
spec2d_data = loader_spectrum2d(row[colname_spectrum2d])
image_basename = os.path.basename(row[colname_cutout])
if image_basename == "None":
image_data = None
else:
image_data = loader_cutout(row[colname_cutout])
self._update_data_components(spec1d_data, key='spectrum1d')
self._update_data_components(spec2d_data, key='spectrum2d')
self._update_data_components(image_data, key='cutout')
self.level2_data = level2_data
self.spec2d_data = spec2d_data
self.render_data(row, spec1d_data, spec2d_data, image_data, level2_data)
def load_exposure(self, index):
'''
Loads the level 2 exposure into the 2D spectrum plot widget.
It can also load back the level 3 spectrum.
'''
name = self.toolbar.exposure_select.currentText()
if 'Level 3' in name:
self.spectrum2d_widget.set_image(
image = self.spec2d_data.get_component(self.spec2d_data.id['Flux']).data,
interpolation = 'none',
aspect = 'auto',
extent = self.extent,
origin='lower')
else:
if name in [component.label for component in self.level2_data.components]:
self.spectrum2d_widget.set_image(
image = self.level2_data.get_component(self.level2_data.id[name]).data,
interpolation = 'none',
aspect = 'auto',
extent = self.extent, origin='lower')
def _update_data_components(self, data, key):
"""
Update the data components that act as containers for the displayed
data in the MOSViz viewer. This obviates the need to keep creating new
data components.
Parameters
----------
data : :class:`glue.core.data.Data`
Data object to replace within the component.
key : str
References the particular data set type.
"""
cur_data = self._loaded_data.get(key, None)
if cur_data is not None and data is None:
self._loaded_data[key] = None
self.session.data_collection.remove(cur_data)
elif cur_data is None and data is not None:
self._loaded_data[key] = data
self.session.data_collection.append(data)
elif data is not None:
cur_data.update_values_from_data(data)
else:
return
def add_slit(self, row=None, width=None, length=None):
if row is None:
row = self.current_row
wcs = self.cutout_wcs
if wcs is None:
raise Exception("Image viewer has no WCS information")
ra = row[self.catalog.meta["special_columns"]["slit_ra"]]
dec = row[self.catalog.meta["special_columns"]["slit_dec"]]
if width is None:
width = row[self.catalog.meta["special_columns"]["slit_width"]]
if length is None:
length = row[self.catalog.meta["special_columns"]["slit_length"]]
self.slit_controller.add_rectangle_sky_slit(wcs, ra, dec, width, length)
def render_data(self, row, spec1d_data=None, spec2d_data=None,
image_data=None, level2_data=None):
"""
Render the updated data sets in the individual plot widgets within the
MOSViz viewer.
"""
self._check_unsaved_comments()
self.image_viewer_hidden = image_data is None
if spec1d_data is not None:
# TODO: This should not be needed. Must explore why the core model
# is out of sync with the proxy model.
self.spectrum1d_widget.plot_widget.clear_plots()
# Clear the specviz model of any rendered plot items
self._specviz_viewer.model.clear()
# Create a new Spectrum1D object from the flux data attribute of
# the incoming data
spec = glue_data_to_spectrum1d(spec1d_data, 'Flux')
# Create a DataItem from the Spectrum1D object, which adds the data
# to the internel specviz model
data_item = self._specviz_viewer.model.add_data(spec, 'Spectrum1D')
# Get the PlotDataItem rendered via the plot's proxy model and
# ensure that it is visible in the plot
plot_data_item = self.spectrum1d_widget.proxy_model.item_from_id(data_item.identifier)
plot_data_item.visible = True
plot_data_item.color = "#000000"
# Explicitly let the plot widget know that data items have changed
self.spectrum1d_widget.plot_widget.on_item_changed(data_item)
if not self.image_viewer_hidden:
if not self.image_widget.isVisible():
self.image_widget.setVisible(True)
wcs = image_data.coords.wcs
self.cutout_wcs = wcs
array = image_data.get_component(image_data.id['Flux']).data
# Add the slit patch to the plot
self.slit_controller.clear_slits()
if "slit_width" in self.catalog.meta["special_columns"] and \
"slit_length" in self.catalog.meta["special_columns"] and \
wcs is not None:
self.add_slit(row)
self.image_widget.draw_slit()
else:
self.image_widget.reset_limits()
self.image_widget.set_image(array, wcs=wcs, interpolation='none', origin='lower')
self.image_widget.axes.set_xlabel("Spatial X")
self.image_widget.axes.set_ylabel("Spatial Y")
if self.slit_controller.has_slits:
self.image_widget.set_slit_limits()
self.image_widget._redraw()
else:
self.cutout_wcs = None
# Plot the 2D spectrum data last because by then we can make sure that
# we set up the extent of the image appropriately if the cutout and the
# 1D spectrum are present so that the axes can be locked.
# We are repurposing the spectrum 2d widget to handle the display of both
# the level 3 and level 2 spectra.
if spec2d_data is not None or level2_data is not None:
self._load_spectrum2d_widget(spec2d_data, level2_data)
else:
self.spectrum2d_widget.no_data()
# Clear the meta information widget
# NOTE: this process is inefficient
for i in range(self.meta_form_layout.count()):
wid = self.meta_form_layout.itemAt(i).widget()
label = self.meta_form_layout.labelForField(wid)
if label is not None:
label.deleteLater()
wid.deleteLater()
# Repopulate the form layout
# NOTE: this process is inefficient
for col in row.colnames:
if col.lower() not in ["comments", "flag"]:
line_edit = QLineEdit(str(row[col]),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow(col, line_edit)
# Set up comment and flag input/display boxes
if self.comments:
if self.savepath is not None:
if self.savepath == -1:
line_edit = QLineEdit(os.path.basename("Not Saving to File."),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
else:
line_edit = QLineEdit(os.path.basename(self.savepath),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
self.input_flag = QLineEdit(self.get_flag(),
self.central_widget.meta_form_widget)
self.input_flag.textChanged.connect(self._text_changed)
self.input_flag.setStyleSheet("background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Flag", self.input_flag)
self.input_comments = QPlainTextEdit(self.get_comment(),
self.central_widget.meta_form_widget)
self.input_comments.textChanged.connect(self._text_changed)
self.input_comments.setStyleSheet("background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Comments", self.input_comments)
self.input_save = QPushButton('Save',
self.central_widget.meta_form_widget)
self.input_save.clicked.connect(self.update_comments)
self.input_save.setDefault(True)
self.input_refresh = QPushButton('Reload',
self.central_widget.meta_form_widget)
self.input_refresh.clicked.connect(self.refresh_comments)
self.meta_form_layout.addRow(self.input_save, self.input_refresh)
if not self.isHidden() and self.image_viewer_hidden:
self.image_widget.setVisible(False)
def _load_spectrum2d_widget(self, spec2d_data, level2_data):
if not spec2d_data:
return
xp2d = np.arange(spec2d_data.shape[1])
yp2d = np.repeat(0, spec2d_data.shape[1])
spectrum2d_disp, spectrum2d_offset = spec2d_data.coords.pixel2world(xp2d, yp2d)
x_min = spectrum2d_disp.min()
x_max = spectrum2d_disp.max()
if self.slit_controller.has_slits and \
None not in self.slit_controller.y_bounds:
y_min, y_max = self.slit_controller.y_bounds
else:
y_min = -0.5
y_max = spec2d_data.shape[0] - 0.5
self.extent = [x_min, x_max, y_min, y_max]
# By default, displays the level 3 spectrum. The level 2
# data is plotted elsewhere, driven by the exposure_select
# combo box signals.
self.spectrum2d_widget.set_image(
image=spec2d_data.get_component(spec2d_data.id['Flux']).data,
interpolation='none',
aspect='auto',
extent=self.extent,
origin='lower')
self.spectrum2d_widget.axes.set_xlabel("Wavelength")
self.spectrum2d_widget.axes.set_ylabel("Spatial Y")
self.spectrum2d_widget._redraw()
# If the axis are linked between the 1d and 2d views, setting the data
# often ignores the initial bounds and instead uses the bounds of the
# 2d data until the 1d view is moved. Force the 2d viewer to honor
# the 1d view bounds.
self.spectrum1d_widget.plot_widget.getPlotItem().sigXRangeChanged.emit(
None, self.spectrum1d_widget.plot_widget.viewRange()[0])
# Populates the level 2 exposures combo box
if level2_data:
self.toolbar.exposure_select.clear()
self.toolbar.exposure_select.addItems(['Level 3'])
components = level2_data.main_components + level2_data.derived_components
self.toolbar.exposure_select.addItems([component.label for component in components])
self._set_exposure_navigation(0)
else:
self._set_exposure_navigation(None)
@defer_draw
def set_locked_axes(self, x=None, y=None):
# Here we only change the setting if x or y are not None
# since if set_locked_axes is called with eg. x=True, then
# we shouldn't change the y setting.
if x is not None:
if x: # Lock the x axis if x is True
def on_x_range_changed(xlim):
self.spectrum2d_widget.axes.set_xlim(*xlim)
self.spectrum2d_widget._redraw()
self.spectrum1d_widget.plot_widget.getPlotItem().sigXRangeChanged.connect(
lambda a, b: on_x_range_changed(b))
# Call the slot to update the axis linking initially
# FIXME: Currently, this does not work for some reason.
on_x_range_changed(self.spectrum1d_widget.plot_widget.viewRange()[0])
else: # Unlock the x axis if x is False
self.spectrum1d_widget.plot_widget.getPlotItem().sigXRangeChanged.disconnect()
if y is not None:
self.spectrum2d_image_share.sharey = y
self.spectrum2d_widget._redraw()
self.image_widget._redraw()
def layer_view(self):
return self._layer_view
def _text_changed(self):
if self.textChangedAt is None:
i = self.toolbar.source_select.currentIndex()
self.textChangedAt = self._index_hash(i)
def _check_unsaved_comments(self):
if self.textChangedAt is None:
return #Nothing to be changed
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
if self.textChangedAt == i:
self.textChangedAt = None
return #This is a refresh
info = "Comments or flags changed but were not saved. Would you like to save them?"
reply = QMessageBox.question(self, '', info, QMessageBox.Yes | QMessageBox.No)
if reply == QMessageBox.Yes:
self.update_comments(True)
self.textChangedAt = None
def _data_collection_index(self, label):
idx = -1
for i, l in enumerate(self.session.data_collection):
if l.label == label:
idx = i
break
if idx == -1:
return -1
self.data_idx = idx
return idx
def _index_hash(self, i):
"""Local selection index -> Table index"""
if self.mask is not None:
size = self.mask.size
temp = np.arange(size)
return temp[self.mask][i]
else:
return i
def _id_to_index_hash(self, ID, l):
"""Object Name -> Table index"""
for i, name in enumerate(l):
if name == ID:
return i
return None
def get_slit_dimensions_from_file(self):
if self.catalog is None:
return None
if "slit_width" in self.catalog.meta["special_columns"] and \
"slit_length" in self.catalog.meta["special_columns"]:
width = self.current_row[self.catalog.meta["special_columns"]["slit_width"]]
length = self.current_row[self.catalog.meta["special_columns"]["slit_length"]]
return [length, width]
return None
def get_slit_units_from_file(self):
# TODO: Update once units infrastructure is in place
return ["arcsec", "arcsec"]
def get_comment(self):
idx = self.data_idx
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
comp = self.session.data_collection[idx].get_component("comments")
return comp.labels[i]
def get_flag(self):
idx = self.data_idx
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
comp = self.session.data_collection[idx].get_component("flag")
return comp.labels[i]
def send_NumericalDataChangedMessage(self):
idx = self.data_idx
data = self.session.data_collection[idx]
data.hub.broadcast(msg.NumericalDataChangedMessage(data, "comments"))
def refresh_comments(self):
self.input_flag.setText(self.get_flag())
self.input_comments.setPlainText(self.get_comment())
self.input_flag.setStyleSheet("background-color: rgba(255, 255, 255);")
self.textChangedAt = None
def _get_save_path(self):
"""
Try to get save path from other MOSVizViewer instances
"""
for v in self.session.application.viewers[0]:
if isinstance(v, MOSVizViewer):
if v.savepath is not None:
if v.data_idx == self.data_idx:
self.savepath = v.savepath
break
def _setup_save_path(self):
"""
Prompt the user for a file to save comments and flags into.
"""
fail = True
success = False
info = "Where would you like to save comments and flags?"
option = pick_item([0, 1],
[os.path.basename(self.filepath), "New MOSViz Table file"],
label=info, title="Comment Setup")
if option == 0:
self.savepath = self.filepath
elif option == 1:
dirname = os.path.dirname(self.filepath)
path = compat.getsavefilename(caption="New MOSViz Table File",
basedir=dirname, filters="*.txt")[0]
if path == "":
return fail
self.savepath = path
else:
return fail
for v in self.session.application.viewers[0]:
if isinstance(v, MOSVizViewer):
if v.data_idx == self.data_idx:
v.savepath = self.savepath
self._layer_view.refresh()
return success
def update_comments(self, pastSelection = False):
"""
Process comment and flag changes and save to file.
Parameters
----------
pastSelection : bool
True when updating past selections. Used when
user forgets to save.
"""
if self.input_flag.text() == "":
self.input_flag.setStyleSheet("background-color: rgba(255, 0, 0);")
return
i = None
try:
i = int(self.input_flag.text())
except ValueError:
self.input_flag.setStyleSheet("background-color: rgba(255, 0, 0);")
info = QMessageBox.information(self, "Status:", "Flag must be an int!")
return
self.input_flag.setStyleSheet("background-color: rgba(255, 255, 255);")
idx = self.data_idx
if pastSelection:
i = self.textChangedAt
self.textChangedAt = None
else:
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
data = self.session.data_collection[idx]
comp = data.get_component("comments")
comp.labels.flags.writeable = True
comp.labels[i] = self.input_comments.toPlainText()
comp = data.get_component("flag")
comp.labels.flags.writeable = True
comp.labels[i] = self.input_flag.text()
self.send_NumericalDataChangedMessage()
self.write_comments()
self.textChangedAt = None
def _load_comments(self, label):
"""
Populate the comments and flag columns.
Attempt to load comments from file.
Parameters
----------
label : str
The label of the data in
session.data_collection.
"""
#Make sure its the right data
#(beacuse subset data is masked)
idx = self._data_collection_index(label)
if idx == -1:
return False
data = self.session.data_collection[idx]
#Fill in default comments:
length = data.shape[0]
new_comments = np.array(["" for i in range(length)], dtype=object)
new_flags = np.array(["0" for i in range(length)], dtype=object)
#Fill in any saved comments:
meta = data.meta
obj_names = data.get_component(self.catalog.meta["special_columns"]["source_id"]).labels
if "MOSViz_comments" in meta.keys():
try:
comments = meta["MOSViz_comments"]
for key in comments.keys():
index = self._id_to_index_hash(key, obj_names)
if index is not None:
line = comments[key]
new_comments[index] = line
except Exception as e:
print("MOSViz Comment Load Failed: ", e)
if "MOSViz_flags" in meta.keys():
try:
flags = meta["MOSViz_flags"]
for key in flags.keys():
index = self._id_to_index_hash(key, obj_names)
if index is not None:
line = flags[key]
new_flags[index] = line
except Exception as e:
print("MOSViz Flag Load Failed: ", e)
#Send to DC
data.add_component(CategoricalComponent(new_flags, "flag"), "flag")
data.add_component(CategoricalComponent(new_comments, "comments"), "comments")
return True
def write_comments(self):
"""
Setup save file. Write comments and flags to file
"""
if self.savepath is None:
fail = self._setup_save_path()
if fail: return
if self.savepath == -1:
return #Do not save to file option
idx = self.data_idx
data = self.session.data_collection[idx]
save_comments = data.get_component("comments").labels
save_flag = data.get_component("flag").labels
obj_names = data.get_component(self.catalog.meta["special_columns"]["source_id"]).labels
fn = self.savepath
folder = os.path.dirname(fn)
t = astropy_table.data_to_astropy_table(data)
#Check if load and save dir paths match
temp = os.path.dirname(self.filepath)
if not os.path.samefile(folder, temp):
t['spectrum1d'].flags.writeable = True
t['spectrum2d'].flags.writeable = True
t['cutout'].flags.writeable = True
for i in range(len(t)):
t['spectrum1d'][i] = os.path.abspath(t['spectrum1d'][i])
t['spectrum2d'][i] = os.path.abspath(t['spectrum2d'][i])
t['cutout'][i] = os.path.abspath(t['cutout'][i])
try:
t.remove_column("comments")
t.remove_column("flag")
keys = t.meta.keys()
if "MOSViz_comments" in keys:
t.meta.pop("MOSViz_comments")
if "MOSViz_flags" in keys:
t.meta.pop("MOSViz_flags")
comments = OrderedDict()
flags = OrderedDict()
for i, line in enumerate(save_comments):
if line != "":
line = line.replace("\n", " ")
key = str(obj_names[i])
comments[key] = line
for i, line in enumerate(save_flag):
if line != "0" and line != "":
line = comments.replace("\n", " ")
key = str(obj_names[i])
flags[key] = line
if len(comments) > 0:
t.meta["MOSViz_comments"] = comments
if len(flags) > 0:
t.meta["MOSViz_flags"] = flags
t.write(fn, format="ascii.ecsv", overwrite=True)
except Exception as e:
print("Comment write failed:", e)
def closeEvent(self, event):
"""
Clean up the extraneous data components created when opening the
MOSViz viewer by overriding the parent class's close event.
"""
super(MOSVizViewer, self).closeEvent(event)
for data in self._loaded_data.values():
self.session.data_collection.remove(data)
class PyDMLogDisplay(QWidget, LogLevels):
"""
Standard display for Log Output
This widget handles instantating a ``GuiHandler`` and displaying log
messages to a ``QPlainTextEdit``. The level of the log can be changed from
inside the widget itself, allowing users to select from any of the
``.levels`` specified by the widget.
Parameters
----------
parent : QObject, optional
logname : str
Name of log to display in widget
level : logging.Level
Initial level of log display
"""
Q_ENUMS(LogLevels)
LogLevels = LogLevels
terminator = '\n'
default_format = '%(asctime)s %(message)s'
default_level = logging.INFO
def __init__(self, parent=None, logname=None, level=logging.NOTSET):
QWidget.__init__(self, parent=parent)
# Create Widgets
self.label = QLabel('Minimum displayed log level: ', parent=self)
self.combo = QComboBox(parent=self)
self.text = QPlainTextEdit(parent=self)
self.text.setReadOnly(True)
self.clear_btn = QPushButton("Clear", parent=self)
# Create layout
layout = QVBoxLayout()
level_control = QHBoxLayout()
level_control.addWidget(self.label)
level_control.addWidget(self.combo)
layout.addLayout(level_control)
layout.addWidget(self.text)
layout.addWidget(self.clear_btn)
self.setLayout(layout)
# Allow QCombobox to control log level
for log_level, value in LogLevels.as_dict().items():
self.combo.addItem(log_level, value)
self.combo.currentIndexChanged[str].connect(self.setLevel)
# Allow QPushButton to clear log text
self.clear_btn.clicked.connect(self.clear)
# Create a handler with the default format
self.handler = GuiHandler(level=level, parent=self)
self.logFormat = self.default_format
self.handler.message.connect(self.write)
# Create logger. Either as a root or given logname
self.log = None
self.level = None
self.logName = logname or ''
self.logLevel = level
self.destroyed.connect(functools.partial(logger_destroyed, self.log))
def sizeHint(self):
return QSize(400, 300)
@Property(LogLevels)
def logLevel(self):
return self.level
@logLevel.setter
def logLevel(self, level):
if level != self.level:
self.level = level
idx = self.combo.findData(level)
self.combo.setCurrentIndex(idx)
@Property(str)
def logName(self):
"""Name of associated log"""
return self.log.name
@logName.setter
def logName(self, name):
# Disconnect prior log from handler
if self.log:
self.log.removeHandler(self.handler)
# Reattach handler to new handler
self.log = logging.getLogger(name)
# Ensure that the log matches level of handler
# only if the handler level is less than the log.
if self.log.level < self.handler.level:
self.log.setLevel(self.handler.level)
# Attach preconfigured handler
self.log.addHandler(self.handler)
@Property(str)
def logFormat(self):
"""Format for log messages"""
return self.handler.formatter._fmt
@logFormat.setter
def logFormat(self, fmt):
self.handler.setFormatter(logging.Formatter(fmt))
@Slot(str)
def write(self, message):
"""Write a message to the log display"""
# We split the incoming message by new lines. In prior iterations of
# this widget it was discovered that large blocks of text cause issues
# at the Qt level.
for msg in message.split(self.terminator):
self.text.appendPlainText(msg)
@Slot()
def clear(self):
"""Clear the text area."""
self.text.clear()
@Slot(str)
def setLevel(self, level):
"""Set the level of the contained logger"""
# Get the level from the incoming string specification
try:
level = getattr(logging, level.upper())
except AttributeError as exc:
logger.exception("Invalid logging level specified %s",
level.upper())
else:
# Set the existing handler and logger to this level
self.handler.setLevel(level)
if self.log.level > self.handler.level or self.log.level == logging.NOTSET:
self.log.setLevel(self.handler.level)
class ConfigurePresentationWindow(QWidget):
def __init__(self, parent):
super().__init__()
self.parent = parent
# set title
self.setWindowTitle("Configure Presentation")
# set variables
self.setupVariables()
# setup Hymn Lyrics
from glob import glob
from pathlib import Path
self.books = sorted([
Path(filename).stem
for filename in glob(r"./marvelData/books/Hymn Lyrics*.book")
])
if len(self.books) > 0:
self.setMinimumHeight(550)
# setup interface
self.setupUI()
def setupVariables(self):
pass
def setupUI(self):
from functools import partial
from qtpy.QtCore import Qt
from qtpy.QtWidgets import QHBoxLayout, QFormLayout, QSlider, QPushButton, QPlainTextEdit, QCheckBox, QComboBox
from qtpy.QtWidgets import QRadioButton, QWidget, QVBoxLayout, QListView, QSpacerItem, QSizePolicy
layout = QHBoxLayout()
layout1 = QFormLayout()
self.fontsizeslider = QSlider(Qt.Horizontal)
self.fontsizeslider.setMinimum(1)
self.fontsizeslider.setMaximum(12)
self.fontsizeslider.setTickInterval(2)
self.fontsizeslider.setSingleStep(2)
self.fontsizeslider.setValue(config.presentationFontSize / 0.5)
self.fontsizeslider.setToolTip(str(config.presentationFontSize))
self.fontsizeslider.valueChanged.connect(
self.presentationFontSizeChanged)
layout1.addRow("Font Size", self.fontsizeslider)
self.changecolorbutton = QPushButton()
buttonStyle = "QPushButton {0}background-color: {2}; color: {3};{1}".format(
"{", "}", config.presentationColorOnDarkTheme if config.theme
== "dark" else config.presentationColorOnLightTheme,
"white" if config.theme == "dark" else "black")
self.changecolorbutton.setStyleSheet(buttonStyle)
self.changecolorbutton.setToolTip("Change Color")
self.changecolorbutton.clicked.connect(self.changeColor)
layout1.addRow("Font Color", self.changecolorbutton)
self.marginslider = QSlider(Qt.Horizontal)
self.marginslider.setMinimum(0)
self.marginslider.setMaximum(200)
self.marginslider.setTickInterval(50)
self.marginslider.setSingleStep(50)
self.marginslider.setValue(config.presentationMargin)
self.marginslider.setToolTip(str(config.presentationMargin))
self.marginslider.valueChanged.connect(self.presentationMarginChanged)
layout1.addRow("Margin", self.marginslider)
self.verticalpositionslider = QSlider(Qt.Horizontal)
self.verticalpositionslider.setMinimum(10)
self.verticalpositionslider.setMaximum(90)
self.verticalpositionslider.setTickInterval(10)
self.verticalpositionslider.setSingleStep(10)
self.verticalpositionslider.setValue(
config.presentationVerticalPosition)
self.verticalpositionslider.setToolTip(
str(config.presentationVerticalPosition))
self.verticalpositionslider.valueChanged.connect(
self.presentationVerticalPositionChanged)
layout1.addRow("Vertical Position", self.verticalpositionslider)
self.horizontalpositionslider = QSlider(Qt.Horizontal)
self.horizontalpositionslider.setMinimum(10)
self.horizontalpositionslider.setMaximum(90)
self.horizontalpositionslider.setTickInterval(10)
self.horizontalpositionslider.setSingleStep(10)
self.horizontalpositionslider.setValue(
config.presentationHorizontalPosition)
self.horizontalpositionslider.setToolTip(
str(config.presentationHorizontalPosition))
self.horizontalpositionslider.valueChanged.connect(
self.presentationHorizontalPositionChanged)
layout1.addRow("Horizontal Position", self.horizontalpositionslider)
self.showBibleSelection = QRadioButton()
self.showBibleSelection.setChecked(True)
self.showBibleSelection.clicked.connect(
lambda: self.selectRadio("bible"))
layout1.addRow("Bible", self.showBibleSelection)
if len(self.books) > 0:
self.showHymnsSelection = QRadioButton()
self.showHymnsSelection.setChecked(False)
self.showHymnsSelection.clicked.connect(
lambda: self.selectRadio("hymns"))
layout1.addRow("Hymns", self.showHymnsSelection)
# Second column
layout2 = QVBoxLayout()
self.bibleWidget = QWidget()
self.bibleLayout = QFormLayout()
checkbox = QCheckBox()
checkbox.setText("")
checkbox.setChecked(config.presentationParser)
checkbox.stateChanged.connect(self.presentationParserChanged)
checkbox.setToolTip("Parse bible verse reference in the entered text")
self.bibleLayout.addRow("Bible Reference", checkbox)
versionCombo = QComboBox()
self.bibleVersions = self.parent.textList
versionCombo.addItems(self.bibleVersions)
initialIndex = 0
if config.mainText in self.bibleVersions:
initialIndex = self.bibleVersions.index(config.mainText)
versionCombo.setCurrentIndex(initialIndex)
versionCombo.currentIndexChanged.connect(self.changeBibleVersion)
self.bibleLayout.addRow("Bible Version", versionCombo)
self.textEntry = QPlainTextEdit("John 3:16; Rm 5:8")
self.bibleLayout.addRow(self.textEntry)
button = QPushButton("Presentation")
button.setToolTip("Go to Presentation")
button.clicked.connect(self.goToPresentation)
self.bibleLayout.addWidget(button)
self.bibleLayout.addItem(
QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding))
self.bibleWidget.setLayout(self.bibleLayout)
self.hymnWidget = QWidget()
self.hymnLayout = QFormLayout()
selected = 0
book = "Hymn Lyrics - English"
if book in self.books:
selected = self.books.index(book)
self.bookList = QComboBox()
self.bookList.addItems(self.books)
self.bookList.setCurrentIndex(selected)
self.bookList.currentIndexChanged.connect(self.selectHymnBook)
self.hymnLayout.addWidget(self.bookList)
self.chapterlist = QListView()
self.chapterlist.clicked.connect(self.selectHymn)
# self.chapterlist.selectionModel().selectionChanged.connect(self.selectHymn)
self.hymnLayout.addWidget(self.chapterlist)
self.buttons = []
for count in range(0, 10):
hymnButton = QPushButton()
hymnButton.setText(" ")
hymnButton.setEnabled(False)
hymnButton.clicked.connect(partial(self.selectParagraph, count))
self.hymnLayout.addWidget(hymnButton)
self.buttons.append(hymnButton)
self.selectHymnBook(selected)
self.hymnWidget.setLayout(self.hymnLayout)
self.hymnWidget.hide()
layout2.addWidget(self.bibleWidget)
if len(self.books) > 0:
layout2.addWidget(self.hymnWidget)
layout.addLayout(layout1)
layout.addLayout(layout2)
self.setLayout(layout)
def selectRadio(self, option):
if option == "bible":
self.bibleWidget.show()
if len(self.books) > 0:
self.hymnWidget.hide()
elif option == "hymns":
self.bibleWidget.hide()
if len(self.books) > 0:
self.hymnWidget.show()
def selectHymnBook(self, option):
from ToolsSqlite import Book
from qtpy.QtCore import QStringListModel
if len(self.books) > 0:
self.hymnBook = self.books[option]
self.hymns = sorted(Book(self.hymnBook).getTopicList())
self.chapterModel = QStringListModel(self.hymns)
self.chapterlist.setModel(self.chapterModel)
def selectHymn(self, option):
from ToolsSqlite import Book
row = option.row()
self.hymn = self.hymns[row]
book = Book(self.hymnBook)
sections = book.getParagraphSectionsByChapter(self.hymn)
count = 0
for button in self.buttons:
if count < len(sections):
section = sections[count]
text = section.replace("<br>", "")[:30]
button.setText(text)
button.setEnabled(True)
else:
button.setText(" ")
button.setEnabled(False)
count += 1
def selectParagraph(self, paragraph):
command = "SCREENBOOK:::{0}:::{1}:::{2}".format(
self.hymnBook, self.hymn, paragraph)
self.parent.runTextCommand(command)
def goToPresentation(self):
command = "SCREEN:::{0}".format(self.textEntry.toPlainText())
self.parent.runTextCommand(command)
def changeColor(self):
from qtpy.QtGui import QColor
from qtpy.QtWidgets import QColorDialog
color = QColorDialog.getColor(
QColor(config.presentationColorOnDarkTheme if config.theme ==
"dark" else config.presentationColorOnLightTheme), self)
if color.isValid():
colorName = color.name()
if config.theme == "dark":
config.presentationColorOnDarkTheme = colorName
else:
config.presentationColorOnLightTheme = colorName
buttonStyle = "QPushButton {0}background-color: {2}; color: {3};{1}".format(
"{", "}", colorName,
"white" if config.theme == "dark" else "black")
self.changecolorbutton.setStyleSheet(buttonStyle)
def presentationFontSizeChanged(self, value):
config.presentationFontSize = value * 0.5
self.fontsizeslider.setToolTip(str(config.presentationFontSize))
def presentationMarginChanged(self, value):
config.presentationMargin = value
self.marginslider.setToolTip(str(config.presentationMargin))
def presentationVerticalPositionChanged(self, value):
config.presentationVerticalPosition = value
self.verticalpositionslider.setToolTip(
str(config.presentationVerticalPosition))
def presentationHorizontalPositionChanged(self, value):
config.presentationHorizontalPosition = value
self.horizontalpositionslider.setValue(
config.presentationHorizontalPosition)
def presentationParserChanged(self):
config.presentationParser = not config.presentationParser
def changeBibleVersion(self, index):
if __name__ == '__main__':
config.mainText = self.bibleVersions[index]
else:
command = "TEXT:::{0}".format(self.bibleVersions[index])
self.parent.runTextCommand(command)
class MOSVizViewer(DataViewer):
LABEL = "MOSViz Viewer"
window_closed = Signal()
_toolbar_cls = MOSViewerToolbar
tools = []
subtools = []
def __init__(self, session, parent=None):
super(MOSVizViewer, self).__init__(session, parent=parent)
self.slit_controller = SlitController(self)
self.load_ui()
# Define some data containers
self.filepath = None
self.savepath = None
self.data_idx = None
self.comments = False
self.textChangedAt = None
self.mask = None
self.cutout_wcs = None
self.level2_data = None
self.spec2d_data = None
self.catalog = None
self.current_row = None
self._specviz_instance = None
self._loaded_data = {}
self._primary_data = None
self._layer_view = SimpleLayerWidget(parent=self)
self._layer_view.layer_combo.currentIndexChanged.connect(
self._selection_changed)
self.resize(800, 600)
self.image_viewer_hidden = False
def load_ui(self):
"""
Setup the MOSView viewer interface.
"""
self.central_widget = QWidget(self)
path = os.path.join(UI_DIR, 'mos_widget.ui')
loadUi(path, self.central_widget)
self.image_widget = DrawableImageWidget(
slit_controller=self.slit_controller)
self.spectrum2d_widget = Spectrum2DWidget()
self._specviz_viewer = Workspace()
self._specviz_viewer.add_plot_window()
self.spectrum1d_widget = self._specviz_viewer.current_plot_window
self.spectrum1d_widget.plot_widget.getPlotItem(
).layout.setContentsMargins(45, 0, 25, 0)
# Set up helper for sharing axes. SharedAxisHelper defaults to no sharing
# and we control the sharing later by setting .sharex and .sharey on the
# helper
self.spectrum2d_image_share = SharedAxisHelper(
self.spectrum2d_widget._axes, self.image_widget._axes)
# We only need to set the image widget to keep the same aspect ratio
# since the two other viewers don't require square pixels, so the axes
# should not change shape.
self.image_widget._axes.set_adjustable('datalim')
self.meta_form_layout = self.central_widget.meta_form_layout
self.meta_form_layout.setFieldGrowthPolicy(
self.meta_form_layout.ExpandingFieldsGrow)
self.central_widget.left_vertical_splitter.insertWidget(
0, self.image_widget)
self.central_widget.right_vertical_splitter.addWidget(
self.spectrum2d_widget)
self.central_widget.right_vertical_splitter.addWidget(
self.spectrum1d_widget.widget())
# Set the splitter stretch factors
self.central_widget.left_vertical_splitter.setStretchFactor(0, 1)
self.central_widget.left_vertical_splitter.setStretchFactor(1, 8)
self.central_widget.right_vertical_splitter.setStretchFactor(0, 1)
self.central_widget.right_vertical_splitter.setStretchFactor(1, 2)
self.central_widget.horizontal_splitter.setStretchFactor(0, 1)
self.central_widget.horizontal_splitter.setStretchFactor(1, 2)
# Keep the left and right splitters in sync otherwise the axes don't line up
self.central_widget.left_vertical_splitter.splitterMoved.connect(
self._left_splitter_moved)
self.central_widget.right_vertical_splitter.splitterMoved.connect(
self._right_splitter_moved)
# Set the central widget
self.setCentralWidget(self.central_widget)
self.central_widget.show()
# Define the options widget
self._options_widget = OptionsWidget()
def show(self, *args, **kwargs):
super(MOSVizViewer, self).show(*args, **kwargs)
# Trigger a sync between the splitters
self._left_splitter_moved()
if self.image_viewer_hidden:
self.image_widget.hide()
else:
self.image_widget.show()
@avoid_circular
def _right_splitter_moved(self, *args, **kwargs):
if self.image_widget.isHidden():
return
sizes = self.central_widget.right_vertical_splitter.sizes()
if sizes == [0, 0]:
sizes = [230, 230]
self.central_widget.left_vertical_splitter.setSizes(sizes)
@avoid_circular
def _left_splitter_moved(self, *args, **kwargs):
if self.image_widget.isHidden():
return
sizes = self.central_widget.left_vertical_splitter.sizes()
if sizes == [0, 0]:
sizes = [230, 230]
self.central_widget.right_vertical_splitter.setSizes(sizes)
def setup_connections(self):
"""
Connects gui elements to event calls.
"""
# Connect the selection event for the combo box to what's displayed
self.toolbar.source_select.currentIndexChanged[int].connect(
lambda ind: self.load_selection(self.catalog[ind]))
self.toolbar.source_select.currentIndexChanged[int].connect(
lambda ind: self._set_navigation(ind))
# Connect the exposure selection event
self.toolbar.exposure_select.currentIndexChanged[int].connect(
lambda ind: self.load_exposure(ind))
self.toolbar.exposure_select.currentIndexChanged[int].connect(
lambda ind: self._set_exposure_navigation(ind))
# Connect the specviz button
if SpecvizDataViewer is not None:
self.toolbar.open_specviz.triggered.connect(
lambda: self._open_in_specviz())
else:
self.toolbar.open_specviz.setDisabled(True)
# Connect slit previous and next buttons
self.toolbar.cycle_next_action.triggered.connect(
lambda: self._set_navigation(self.toolbar.source_select.
currentIndex() + 1))
self.toolbar.cycle_previous_action.triggered.connect(
lambda: self._set_navigation(self.toolbar.source_select.
currentIndex() - 1))
# Connect exposure previous and next buttons
self.toolbar.exposure_next_action.triggered.connect(
lambda: self._set_exposure_navigation(self.toolbar.exposure_select.
currentIndex() + 1))
self.toolbar.exposure_previous_action.triggered.connect(
lambda: self._set_exposure_navigation(self.toolbar.exposure_select.
currentIndex() - 1))
# Connect the toolbar axes setting actions
self.toolbar.lock_x_action.triggered.connect(
lambda state: self.set_locked_axes(x=state))
self.toolbar.lock_y_action.triggered.connect(
lambda state: self.set_locked_axes(y=state))
def options_widget(self):
return self._options_widget
def initialize_toolbar(self):
"""
Initialize the custom toolbar for the MOSViz viewer.
"""
from glue.config import viewer_tool
self.toolbar = self._toolbar_cls(self)
for tool_id in self.tools:
mode_cls = viewer_tool.members[tool_id]
mode = mode_cls(self)
self.toolbar.add_tool(mode)
self.addToolBar(self.toolbar)
self.setup_connections()
def register_to_hub(self, hub):
super(MOSVizViewer, self).register_to_hub(hub)
def has_data_or_subset(x):
if x.sender is self._primary_data:
return True
elif isinstance(x.sender,
Subset) and x.sender.data is self._primary_data:
return True
else:
return False
hub.subscribe(self,
msg.SubsetCreateMessage,
handler=self._add_subset,
filter=has_data_or_subset)
hub.subscribe(self,
msg.SubsetUpdateMessage,
handler=self._update_subset,
filter=has_data_or_subset)
hub.subscribe(self,
msg.SubsetDeleteMessage,
handler=self._remove_subset,
filter=has_data_or_subset)
hub.subscribe(self,
msg.DataUpdateMessage,
handler=self._update_data,
filter=has_data_or_subset)
def add_data(self, data):
"""
Processes data message from the central communication hub.
Parameters
----------
data : :class:`glue.core.data.Data`
Data object.
"""
# Check whether the data is suitable for the MOSViz viewer - basically
# we expect a table of 1D columns with at least three string and four
# floating-point columns.
if data.ndim != 1:
QMessageBox.critical(self,
"Error", "MOSViz viewer can only be used "
"for data with 1-dimensional components",
buttons=QMessageBox.Ok)
return False
components = [data.get_component(cid) for cid in data.main_components]
categorical = [c for c in components if c.categorical]
if len(categorical) < 3:
QMessageBox.critical(
self,
"Error", "MOSViz viewer expected at least "
"three string components/columns, representing "
"the filenames of the 1D and 2D spectra and "
"cutouts",
buttons=QMessageBox.Ok)
return False
# We can relax the following requirement if we make the slit parameters
# optional
numerical = [c for c in components if c.numeric]
if len(numerical) < 4:
QMessageBox.critical(
self,
"Error", "MOSViz viewer expected at least "
"four numerical components/columns, representing "
"the slit position, length, and position angle",
buttons=QMessageBox.Ok)
return False
# Make sure the loaders and column names are correct
result = confirm_loaders_and_column_names(data)
if not result:
return False
self._primary_data = data
self._layer_view.data = data
self._unpack_selection(data)
return True
def add_data_for_testing(self, data):
"""
Processes data message from the central communication hub.
Parameters
----------
data : :class:`glue.core.data.Data`
Data object.
"""
# Check whether the data is suitable for the MOSViz viewer - basically
# we expect a table of 1D columns with at least three string and four
# floating-point columns.
if data.ndim != 1:
QMessageBox.critical(self,
"Error", "MOSViz viewer can only be used "
"for data with 1-dimensional components",
buttons=QMessageBox.Ok)
return False
components = [data.get_component(cid) for cid in data.main_components]
categorical = [c for c in components if c.categorical]
if len(categorical) < 3:
QMessageBox.critical(
self,
"Error", "MOSViz viewer expected at least "
"three string components/columns, representing "
"the filenames of the 1D and 2D spectra and "
"cutouts",
buttons=QMessageBox.Ok)
return False
# We can relax the following requirement if we make the slit parameters
# optional
numerical = [c for c in components if c.numeric]
if len(numerical) < 4:
QMessageBox.critical(
self,
"Error", "MOSViz viewer expected at least "
"four numerical components/columns, representing "
"the slit position, length, and position angle",
buttons=QMessageBox.Ok)
return False
# Block of code to bypass the loader_selection gui
#########################################################
if 'loaders' not in data.meta:
data.meta['loaders'] = {}
# Deimos data
data.meta['loaders']['spectrum1d'] = "DEIMOS 1D Spectrum"
data.meta['loaders']['spectrum2d'] = "DEIMOS 2D Spectrum"
data.meta['loaders']['cutout'] = "ACS Cutout Image"
if 'special_columns' not in data.meta:
data.meta['special_columns'] = {}
data.meta['special_columns']['spectrum1d'] = 'spectrum1d'
data.meta['special_columns']['spectrum2d'] = 'spectrum2d'
data.meta['special_columns']['source_id'] = 'id'
data.meta['special_columns']['cutout'] = 'cutout'
data.meta['special_columns']['slit_ra'] = 'ra'
data.meta['special_columns']['slit_dec'] = 'dec'
data.meta['special_columns']['slit_width'] = 'slit_width'
data.meta['special_columns']['slit_length'] = 'slit_length'
data.meta['loaders_confirmed'] = True
#########################################################
self._primary_data = data
self._layer_view.data = data
self._unpack_selection(data)
return True
def add_subset(self, subset):
"""
Processes subset messages from the central communication hub.
Parameters
----------
subset :
Subset object.
"""
self._layer_view.refresh()
index = self._layer_view.layer_combo.findData(subset)
self._layer_view.layer_combo.setCurrentIndex(index)
return True
def _update_data(self, message):
"""
Update data message.
Parameters
----------
message : :class:`glue.core.message.Message`
Data message object.
"""
self._layer_view.refresh()
def _add_subset(self, message):
"""
Add subset message.
Parameters
----------
message : :class:`glue.core.message.Message`
Subset message object.
"""
self._layer_view.refresh()
def _update_subset(self, message):
"""
Update subset message.
Parameters
----------
message : :class:`glue.core.message.Message`
Update message object.
"""
self._layer_view.refresh()
self._unpack_selection(message.subset)
def _remove_subset(self, message):
"""
Remove subset message.
Parameters
----------
message : :class:`glue.core.message.Message`
Subset message object.
"""
self._layer_view.refresh()
self._unpack_selection(message.subset.data)
def _selection_changed(self):
self._unpack_selection(self._layer_view.layer_combo.currentData())
def _unpack_selection(self, data):
"""
Interprets the :class:`glue.core.data.Data` object by decomposing the
data elements, extracting relevant data, and recomposing a
package-agnostic dictionary object containing the relevant data.
Parameters
----------
data : :class:`glue.core.data.Data`
Glue data object to decompose.
"""
mask = None
if isinstance(data, Subset):
try:
mask = data.to_mask()
except IncompatibleAttribute:
return
if not np.any(mask):
return
data = data.data
self.mask = mask
# Clear the table
self.catalog = Table()
self.catalog.meta = data.meta
self.comments = False
col_names = data.components
for att in col_names:
cid = data.id[att]
component = data.get_component(cid)
if component.categorical:
comp_labels = component.labels[mask]
if comp_labels.ndim > 1:
comp_labels = comp_labels[0]
if str(att) in ["comments", "flag"]:
self.comments = True
elif str(att) in [
'level2', 'spectrum1d', 'spectrum2d', 'cutout'
]:
self.filepath = component._load_log.path
p = Path(self.filepath)
path = os.path.sep.join(p.parts[:-1])
self.catalog[str(att)] = [
os.path.join(path, x) for x in comp_labels
]
else:
self.catalog[str(att)] = comp_labels
else:
comp_data = component.data[mask]
if comp_data.ndim > 1:
comp_data = comp_data[0]
self.catalog[str(att)] = comp_data
if len(self.catalog) > 0:
if not self.comments:
self.comments = self._load_comments(data.label) #Returns bool
else:
self._data_collection_index(data.label)
self._get_save_path()
# Update gui elements
self._update_navigation(select=0)
def _update_navigation(self, select=0):
"""
Updates the :class:`qtpy.QtWidgets.QComboBox` widget with the
appropriate source `id`s from the MOS catalog.
"""
if self.toolbar is None:
return
self.toolbar.source_select.blockSignals(True)
self.toolbar.source_select.clear()
if len(self.catalog) > 0 and self.catalog.meta["special_columns"][
"source_id"] in self.catalog.colnames:
self.toolbar.source_select.addItems(self.catalog[
self.catalog.meta["special_columns"]["source_id"]][:])
self.toolbar.source_select.setCurrentIndex(select)
self.toolbar.source_select.blockSignals(False)
self.toolbar.source_select.currentIndexChanged.emit(select)
def _set_navigation(self, index):
if len(self.catalog) < index:
return
if 0 <= index < self.toolbar.source_select.count():
self.toolbar.source_select.setCurrentIndex(index)
if index <= 0:
self.toolbar.cycle_previous_action.setDisabled(True)
else:
self.toolbar.cycle_previous_action.setDisabled(False)
if index >= self.toolbar.source_select.count() - 1:
self.toolbar.cycle_next_action.setDisabled(True)
else:
self.toolbar.cycle_next_action.setDisabled(False)
def _set_exposure_navigation(self, index):
# For level 3-only data.
if index == None:
# for some unknown reason (related to layout
# managers perhaps?), the combo box does not
# disappear from screen even when forced to
# hide. Next best solution is to disable it.
self.toolbar.exposure_select.setEnabled(False)
self.toolbar.exposure_next_action.setEnabled(False)
self.toolbar.exposure_previous_action.setEnabled(False)
return
if index > self.toolbar.exposure_select.count():
return
if 0 <= index < self.toolbar.exposure_select.count():
self.toolbar.exposure_select.setCurrentIndex(index)
if index < 1:
self.toolbar.exposure_previous_action.setEnabled(False)
else:
self.toolbar.exposure_previous_action.setEnabled(True)
if index >= self.toolbar.exposure_select.count() - 1:
self.toolbar.exposure_next_action.setEnabled(False)
else:
self.toolbar.exposure_next_action.setEnabled(True)
def _open_in_specviz(self):
if self._specviz_instance is None:
# Store a reference to the currently opened data viewer. This means
# new "open in specviz" events will be added to the current viewer
# as opposed to opening a new viewer.
self._specviz_instance = self.session.application.new_data_viewer(
SpecvizDataViewer)
# Clear the reference to ensure no qt dangling pointers
def _clear_instance_reference():
self._specviz_instance = None
self._specviz_instance.window_closed.connect(
_clear_instance_reference)
# Create a new Spectrum1D object from the flux data attribute of
# the incoming data
spec = glue_data_to_spectrum1d(self._loaded_data['spectrum1d'], 'Flux')
# Create a DataItem from the Spectrum1D object, which adds the data
# to the internel specviz model
data_item = self._specviz_instance.current_workspace.model.add_data(
spec, 'Spectrum1D')
self._specviz_instance.current_workspace.force_plot(data_item)
def load_selection(self, row):
"""
Processes a row in the MOS catalog by first loading the data set,
updating the stored data components, and then rendering the data on
the visible MOSViz viewer plots.
Parameters
----------
row : `astropy.table.Row`
A row object representing a row in the MOS catalog. Each key
should be a column name.
"""
self.current_row = row
# Get loaders
loader_spectrum1d = SPECTRUM1D_LOADERS[self.catalog.meta["loaders"]
["spectrum1d"]]
loader_spectrum2d = SPECTRUM2D_LOADERS[self.catalog.meta["loaders"]
["spectrum2d"]]
loader_cutout = CUTOUT_LOADERS[self.catalog.meta["loaders"]["cutout"]]
# Get column names
colname_spectrum1d = self.catalog.meta["special_columns"]["spectrum1d"]
colname_spectrum2d = self.catalog.meta["special_columns"]["spectrum2d"]
colname_cutout = self.catalog.meta["special_columns"]["cutout"]
level2_data = None
if "level2" in self.catalog.meta["loaders"]:
loader_level2 = LEVEL2_LOADERS[self.catalog.meta["loaders"]
["level2"]]
colname_level2 = self.catalog.meta["special_columns"]["level2"]
level2_basename = os.path.basename(row[colname_level2])
if level2_basename != "None":
level2_data = loader_level2(row[colname_level2])
spec1d_basename = os.path.basename(row[colname_spectrum1d])
if spec1d_basename == "None":
spec1d_data = None
else:
spec1d_data = loader_spectrum1d(row[colname_spectrum1d])
spec2d_basename = os.path.basename(row[colname_spectrum2d])
if spec2d_basename == "None":
spec2d_data = None
else:
spec2d_data = loader_spectrum2d(row[colname_spectrum2d])
image_basename = os.path.basename(row[colname_cutout])
if image_basename == "None":
image_data = None
else:
image_data = loader_cutout(row[colname_cutout])
self._update_data_components(spec1d_data, key='spectrum1d')
self._update_data_components(spec2d_data, key='spectrum2d')
self._update_data_components(image_data, key='cutout')
self.level2_data = level2_data
self.spec2d_data = spec2d_data
self.render_data(row, spec1d_data, spec2d_data, image_data,
level2_data)
def load_exposure(self, index):
'''
Loads the level 2 exposure into the 2D spectrum plot widget.
It can also load back the level 3 spectrum.
'''
name = self.toolbar.exposure_select.currentText()
if 'Level 3' in name:
self.spectrum2d_widget.set_image(
image=self.spec2d_data.get_component(
self.spec2d_data.id['Flux']).data,
interpolation='none',
aspect='auto',
extent=self.extent,
origin='lower')
else:
if name in [
component.label
for component in self.level2_data.components
]:
self.spectrum2d_widget.set_image(
image=self.level2_data.get_component(
self.level2_data.id[name]).data,
interpolation='none',
aspect='auto',
extent=self.extent,
origin='lower')
def _update_data_components(self, data, key):
"""
Update the data components that act as containers for the displayed
data in the MOSViz viewer. This obviates the need to keep creating new
data components.
Parameters
----------
data : :class:`glue.core.data.Data`
Data object to replace within the component.
key : str
References the particular data set type.
"""
cur_data = self._loaded_data.get(key, None)
if cur_data is not None and data is None:
self._loaded_data[key] = None
self.session.data_collection.remove(cur_data)
elif cur_data is None and data is not None:
self._loaded_data[key] = data
self.session.data_collection.append(data)
elif data is not None:
cur_data.update_values_from_data(data)
else:
return
def add_slit(self, row=None, width=None, length=None):
if row is None:
row = self.current_row
wcs = self.cutout_wcs
if wcs is None:
raise Exception("Image viewer has no WCS information")
ra = row[self.catalog.meta["special_columns"]["slit_ra"]]
dec = row[self.catalog.meta["special_columns"]["slit_dec"]]
if width is None:
width = row[self.catalog.meta["special_columns"]["slit_width"]]
if length is None:
length = row[self.catalog.meta["special_columns"]["slit_length"]]
self.slit_controller.add_rectangle_sky_slit(wcs, ra, dec, width,
length)
def render_data(self,
row,
spec1d_data=None,
spec2d_data=None,
image_data=None,
level2_data=None):
"""
Render the updated data sets in the individual plot widgets within the
MOSViz viewer.
"""
self._check_unsaved_comments()
self.image_viewer_hidden = image_data is None
if spec1d_data is not None:
# TODO: This should not be needed. Must explore why the core model
# is out of sync with the proxy model.
self.spectrum1d_widget.plot_widget.clear_plots()
# Clear the specviz model of any rendered plot items
self._specviz_viewer.model.clear()
# Create a new Spectrum1D object from the flux data attribute of
# the incoming data
spec = glue_data_to_spectrum1d(spec1d_data, 'Flux')
# Create a DataItem from the Spectrum1D object, which adds the data
# to the internel specviz model
data_item = self._specviz_viewer.model.add_data(spec, 'Spectrum1D')
# Get the PlotDataItem rendered via the plot's proxy model and
# ensure that it is visible in the plot
plot_data_item = self.spectrum1d_widget.proxy_model.item_from_id(
data_item.identifier)
plot_data_item.visible = True
plot_data_item.color = "#000000"
# Explicitly let the plot widget know that data items have changed
self.spectrum1d_widget.plot_widget.on_item_changed(data_item)
if not self.image_viewer_hidden:
if not self.image_widget.isVisible():
self.image_widget.setVisible(True)
wcs = image_data.coords.wcs
self.cutout_wcs = wcs
array = image_data.get_component(image_data.id['Flux']).data
# Add the slit patch to the plot
self.slit_controller.clear_slits()
if "slit_width" in self.catalog.meta["special_columns"] and \
"slit_length" in self.catalog.meta["special_columns"] and \
wcs is not None:
self.add_slit(row)
self.image_widget.draw_slit()
else:
self.image_widget.reset_limits()
self.image_widget.set_image(array,
wcs=wcs,
interpolation='none',
origin='lower')
self.image_widget.axes.set_xlabel("Spatial X")
self.image_widget.axes.set_ylabel("Spatial Y")
if self.slit_controller.has_slits:
self.image_widget.set_slit_limits()
self.image_widget._redraw()
else:
self.cutout_wcs = None
# Plot the 2D spectrum data last because by then we can make sure that
# we set up the extent of the image appropriately if the cutout and the
# 1D spectrum are present so that the axes can be locked.
# We are repurposing the spectrum 2d widget to handle the display of both
# the level 3 and level 2 spectra.
if spec2d_data is not None or level2_data is not None:
self._load_spectrum2d_widget(spec2d_data, level2_data)
else:
self.spectrum2d_widget.no_data()
# Clear the meta information widget
# NOTE: this process is inefficient
for i in range(self.meta_form_layout.count()):
wid = self.meta_form_layout.itemAt(i).widget()
label = self.meta_form_layout.labelForField(wid)
if label is not None:
label.deleteLater()
wid.deleteLater()
# Repopulate the form layout
# NOTE: this process is inefficient
for col in row.colnames:
if col.lower() not in ["comments", "flag"]:
line_edit = QLineEdit(str(row[col]),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow(col, line_edit)
# Set up comment and flag input/display boxes
if self.comments:
if self.savepath is not None:
if self.savepath == -1:
line_edit = QLineEdit(
os.path.basename("Not Saving to File."),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
else:
line_edit = QLineEdit(os.path.basename(self.savepath),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
self.input_flag = QLineEdit(self.get_flag(),
self.central_widget.meta_form_widget)
self.input_flag.textChanged.connect(self._text_changed)
self.input_flag.setStyleSheet(
"background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Flag", self.input_flag)
self.input_comments = QPlainTextEdit(
self.get_comment(), self.central_widget.meta_form_widget)
self.input_comments.textChanged.connect(self._text_changed)
self.input_comments.setStyleSheet(
"background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Comments", self.input_comments)
self.input_save = QPushButton('Save',
self.central_widget.meta_form_widget)
self.input_save.clicked.connect(self.update_comments)
self.input_save.setDefault(True)
self.input_refresh = QPushButton(
'Reload', self.central_widget.meta_form_widget)
self.input_refresh.clicked.connect(self.refresh_comments)
self.meta_form_layout.addRow(self.input_save, self.input_refresh)
if not self.isHidden() and self.image_viewer_hidden:
self.image_widget.setVisible(False)
def _load_spectrum2d_widget(self, spec2d_data, level2_data):
if not spec2d_data:
return
xp2d = np.arange(spec2d_data.shape[1])
yp2d = np.repeat(0, spec2d_data.shape[1])
spectrum2d_disp, spectrum2d_offset = spec2d_data.coords.pixel2world(
xp2d, yp2d)
x_min = spectrum2d_disp.min()
x_max = spectrum2d_disp.max()
if self.slit_controller.has_slits and \
None not in self.slit_controller.y_bounds:
y_min, y_max = self.slit_controller.y_bounds
else:
y_min = -0.5
y_max = spec2d_data.shape[0] - 0.5
self.extent = [x_min, x_max, y_min, y_max]
# By default, displays the level 3 spectrum. The level 2
# data is plotted elsewhere, driven by the exposure_select
# combo box signals.
self.spectrum2d_widget.set_image(image=spec2d_data.get_component(
spec2d_data.id['Flux']).data,
interpolation='none',
aspect='auto',
extent=self.extent,
origin='lower')
self.spectrum2d_widget.axes.set_xlabel("Wavelength")
self.spectrum2d_widget.axes.set_ylabel("Spatial Y")
self.spectrum2d_widget._redraw()
# If the axis are linked between the 1d and 2d views, setting the data
# often ignores the initial bounds and instead uses the bounds of the
# 2d data until the 1d view is moved. Force the 2d viewer to honor
# the 1d view bounds.
self.spectrum1d_widget.plot_widget.getPlotItem().sigXRangeChanged.emit(
None,
self.spectrum1d_widget.plot_widget.viewRange()[0])
# Populates the level 2 exposures combo box
if level2_data:
self.toolbar.exposure_select.clear()
self.toolbar.exposure_select.addItems(['Level 3'])
components = level2_data.main_components + level2_data.derived_components
self.toolbar.exposure_select.addItems(
[component.label for component in components])
self._set_exposure_navigation(0)
else:
self._set_exposure_navigation(None)
@defer_draw
def set_locked_axes(self, x=None, y=None):
# Here we only change the setting if x or y are not None
# since if set_locked_axes is called with eg. x=True, then
# we shouldn't change the y setting.
if x is not None:
if x: # Lock the x axis if x is True
def on_x_range_changed(xlim):
self.spectrum2d_widget.axes.set_xlim(*xlim)
self.spectrum2d_widget._redraw()
self.spectrum1d_widget.plot_widget.getPlotItem(
).sigXRangeChanged.connect(lambda a, b: on_x_range_changed(b))
# Call the slot to update the axis linking initially
# FIXME: Currently, this does not work for some reason.
on_x_range_changed(
self.spectrum1d_widget.plot_widget.viewRange()[0])
else: # Unlock the x axis if x is False
self.spectrum1d_widget.plot_widget.getPlotItem(
).sigXRangeChanged.disconnect()
if y is not None:
self.spectrum2d_image_share.sharey = y
self.spectrum2d_widget._redraw()
self.image_widget._redraw()
def layer_view(self):
return self._layer_view
def _text_changed(self):
if self.textChangedAt is None:
i = self.toolbar.source_select.currentIndex()
self.textChangedAt = self._index_hash(i)
def _check_unsaved_comments(self):
if self.textChangedAt is None:
return #Nothing to be changed
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
if self.textChangedAt == i:
self.textChangedAt = None
return #This is a refresh
info = "Comments or flags changed but were not saved. Would you like to save them?"
reply = QMessageBox.question(self, '', info,
QMessageBox.Yes | QMessageBox.No)
if reply == QMessageBox.Yes:
self.update_comments(True)
self.textChangedAt = None
def _data_collection_index(self, label):
idx = -1
for i, l in enumerate(self.session.data_collection):
if l.label == label:
idx = i
break
if idx == -1:
return -1
self.data_idx = idx
return idx
def _index_hash(self, i):
"""Local selection index -> Table index"""
if self.mask is not None:
size = self.mask.size
temp = np.arange(size)
return temp[self.mask][i]
else:
return i
def _id_to_index_hash(self, ID, l):
"""Object Name -> Table index"""
for i, name in enumerate(l):
if name == ID:
return i
return None
def get_slit_dimensions_from_file(self):
if self.catalog is None:
return None
if "slit_width" in self.catalog.meta["special_columns"] and \
"slit_length" in self.catalog.meta["special_columns"]:
width = self.current_row[self.catalog.meta["special_columns"]
["slit_width"]]
length = self.current_row[self.catalog.meta["special_columns"]
["slit_length"]]
return [length, width]
return None
def get_slit_units_from_file(self):
# TODO: Update once units infrastructure is in place
return ["arcsec", "arcsec"]
def get_comment(self):
idx = self.data_idx
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
comp = self.session.data_collection[idx].get_component("comments")
return comp.labels[i]
def get_flag(self):
idx = self.data_idx
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
comp = self.session.data_collection[idx].get_component("flag")
return comp.labels[i]
def send_NumericalDataChangedMessage(self):
idx = self.data_idx
data = self.session.data_collection[idx]
data.hub.broadcast(msg.NumericalDataChangedMessage(data, "comments"))
def refresh_comments(self):
self.input_flag.setText(self.get_flag())
self.input_comments.setPlainText(self.get_comment())
self.input_flag.setStyleSheet("background-color: rgba(255, 255, 255);")
self.textChangedAt = None
def _get_save_path(self):
"""
Try to get save path from other MOSVizViewer instances
"""
for v in self.session.application.viewers[0]:
if isinstance(v, MOSVizViewer):
if v.savepath is not None:
if v.data_idx == self.data_idx:
self.savepath = v.savepath
break
def _setup_save_path(self):
"""
Prompt the user for a file to save comments and flags into.
"""
fail = True
success = False
info = "Where would you like to save comments and flags?"
option = pick_item(
[0, 1], [os.path.basename(self.filepath), "New MOSViz Table file"],
label=info,
title="Comment Setup")
if option == 0:
self.savepath = self.filepath
elif option == 1:
dirname = os.path.dirname(self.filepath)
path = compat.getsavefilename(caption="New MOSViz Table File",
basedir=dirname,
filters="*.txt")[0]
if path == "":
return fail
self.savepath = path
else:
return fail
for v in self.session.application.viewers[0]:
if isinstance(v, MOSVizViewer):
if v.data_idx == self.data_idx:
v.savepath = self.savepath
self._layer_view.refresh()
return success
def update_comments(self, pastSelection=False):
"""
Process comment and flag changes and save to file.
Parameters
----------
pastSelection : bool
True when updating past selections. Used when
user forgets to save.
"""
if self.input_flag.text() == "":
self.input_flag.setStyleSheet("background-color: rgba(255, 0, 0);")
return
i = None
try:
i = int(self.input_flag.text())
except ValueError:
self.input_flag.setStyleSheet("background-color: rgba(255, 0, 0);")
info = QMessageBox.information(self, "Status:",
"Flag must be an int!")
return
self.input_flag.setStyleSheet("background-color: rgba(255, 255, 255);")
idx = self.data_idx
if pastSelection:
i = self.textChangedAt
self.textChangedAt = None
else:
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
data = self.session.data_collection[idx]
comp = data.get_component("comments")
comp.labels.flags.writeable = True
comp.labels[i] = self.input_comments.toPlainText()
comp = data.get_component("flag")
comp.labels.flags.writeable = True
comp.labels[i] = self.input_flag.text()
self.send_NumericalDataChangedMessage()
self.write_comments()
self.textChangedAt = None
def _load_comments(self, label):
"""
Populate the comments and flag columns.
Attempt to load comments from file.
Parameters
----------
label : str
The label of the data in
session.data_collection.
"""
#Make sure its the right data
#(beacuse subset data is masked)
idx = self._data_collection_index(label)
if idx == -1:
return False
data = self.session.data_collection[idx]
#Fill in default comments:
length = data.shape[0]
new_comments = np.array(["" for i in range(length)], dtype=object)
new_flags = np.array(["0" for i in range(length)], dtype=object)
#Fill in any saved comments:
meta = data.meta
obj_names = data.get_component(
self.catalog.meta["special_columns"]["source_id"]).labels
if "MOSViz_comments" in meta.keys():
try:
comments = meta["MOSViz_comments"]
for key in comments.keys():
index = self._id_to_index_hash(key, obj_names)
if index is not None:
line = comments[key]
new_comments[index] = line
except Exception as e:
print("MOSViz Comment Load Failed: ", e)
if "MOSViz_flags" in meta.keys():
try:
flags = meta["MOSViz_flags"]
for key in flags.keys():
index = self._id_to_index_hash(key, obj_names)
if index is not None:
line = flags[key]
new_flags[index] = line
except Exception as e:
print("MOSViz Flag Load Failed: ", e)
#Send to DC
data.add_component(CategoricalComponent(new_flags, "flag"), "flag")
data.add_component(CategoricalComponent(new_comments, "comments"),
"comments")
return True
def write_comments(self):
"""
Setup save file. Write comments and flags to file
"""
if self.savepath is None:
fail = self._setup_save_path()
if fail: return
if self.savepath == -1:
return #Do not save to file option
idx = self.data_idx
data = self.session.data_collection[idx]
save_comments = data.get_component("comments").labels
save_flag = data.get_component("flag").labels
obj_names = data.get_component(
self.catalog.meta["special_columns"]["source_id"]).labels
fn = self.savepath
folder = os.path.dirname(fn)
t = astropy_table.data_to_astropy_table(data)
#Check if load and save dir paths match
temp = os.path.dirname(self.filepath)
if not os.path.samefile(folder, temp):
t['spectrum1d'].flags.writeable = True
t['spectrum2d'].flags.writeable = True
t['cutout'].flags.writeable = True
for i in range(len(t)):
t['spectrum1d'][i] = os.path.abspath(t['spectrum1d'][i])
t['spectrum2d'][i] = os.path.abspath(t['spectrum2d'][i])
t['cutout'][i] = os.path.abspath(t['cutout'][i])
try:
t.remove_column("comments")
t.remove_column("flag")
keys = t.meta.keys()
if "MOSViz_comments" in keys:
t.meta.pop("MOSViz_comments")
if "MOSViz_flags" in keys:
t.meta.pop("MOSViz_flags")
comments = OrderedDict()
flags = OrderedDict()
for i, line in enumerate(save_comments):
if line != "":
line = line.replace("\n", " ")
key = str(obj_names[i])
comments[key] = line
for i, line in enumerate(save_flag):
if line != "0" and line != "":
line = comments.replace("\n", " ")
key = str(obj_names[i])
flags[key] = line
if len(comments) > 0:
t.meta["MOSViz_comments"] = comments
if len(flags) > 0:
t.meta["MOSViz_flags"] = flags
t.write(fn, format="ascii.ecsv", overwrite=True)
except Exception as e:
print("Comment write failed:", e)
def closeEvent(self, event):
"""
Clean up the extraneous data components created when opening the
MOSViz viewer by overriding the parent class's close event.
"""
super(MOSVizViewer, self).closeEvent(event)
for data in self._loaded_data.values():
self.session.data_collection.remove(data)
def setupUI(self):
from functools import partial
from qtpy.QtCore import Qt
from qtpy.QtWidgets import QHBoxLayout, QFormLayout, QSlider, QPushButton, QPlainTextEdit, QCheckBox, QComboBox
from qtpy.QtWidgets import QRadioButton, QWidget, QVBoxLayout, QListView, QSpacerItem, QSizePolicy
layout = QHBoxLayout()
layout1 = QFormLayout()
self.fontsizeslider = QSlider(Qt.Horizontal)
self.fontsizeslider.setMinimum(1)
self.fontsizeslider.setMaximum(12)
self.fontsizeslider.setTickInterval(2)
self.fontsizeslider.setSingleStep(2)
self.fontsizeslider.setValue(config.presentationFontSize / 0.5)
self.fontsizeslider.setToolTip(str(config.presentationFontSize))
self.fontsizeslider.valueChanged.connect(
self.presentationFontSizeChanged)
layout1.addRow("Font Size", self.fontsizeslider)
self.changecolorbutton = QPushButton()
buttonStyle = "QPushButton {0}background-color: {2}; color: {3};{1}".format(
"{", "}", config.presentationColorOnDarkTheme if config.theme
== "dark" else config.presentationColorOnLightTheme,
"white" if config.theme == "dark" else "black")
self.changecolorbutton.setStyleSheet(buttonStyle)
self.changecolorbutton.setToolTip("Change Color")
self.changecolorbutton.clicked.connect(self.changeColor)
layout1.addRow("Font Color", self.changecolorbutton)
self.marginslider = QSlider(Qt.Horizontal)
self.marginslider.setMinimum(0)
self.marginslider.setMaximum(200)
self.marginslider.setTickInterval(50)
self.marginslider.setSingleStep(50)
self.marginslider.setValue(config.presentationMargin)
self.marginslider.setToolTip(str(config.presentationMargin))
self.marginslider.valueChanged.connect(self.presentationMarginChanged)
layout1.addRow("Margin", self.marginslider)
self.verticalpositionslider = QSlider(Qt.Horizontal)
self.verticalpositionslider.setMinimum(10)
self.verticalpositionslider.setMaximum(90)
self.verticalpositionslider.setTickInterval(10)
self.verticalpositionslider.setSingleStep(10)
self.verticalpositionslider.setValue(
config.presentationVerticalPosition)
self.verticalpositionslider.setToolTip(
str(config.presentationVerticalPosition))
self.verticalpositionslider.valueChanged.connect(
self.presentationVerticalPositionChanged)
layout1.addRow("Vertical Position", self.verticalpositionslider)
self.horizontalpositionslider = QSlider(Qt.Horizontal)
self.horizontalpositionslider.setMinimum(10)
self.horizontalpositionslider.setMaximum(90)
self.horizontalpositionslider.setTickInterval(10)
self.horizontalpositionslider.setSingleStep(10)
self.horizontalpositionslider.setValue(
config.presentationHorizontalPosition)
self.horizontalpositionslider.setToolTip(
str(config.presentationHorizontalPosition))
self.horizontalpositionslider.valueChanged.connect(
self.presentationHorizontalPositionChanged)
layout1.addRow("Horizontal Position", self.horizontalpositionslider)
self.showBibleSelection = QRadioButton()
self.showBibleSelection.setChecked(True)
self.showBibleSelection.clicked.connect(
lambda: self.selectRadio("bible"))
layout1.addRow("Bible", self.showBibleSelection)
if len(self.books) > 0:
self.showHymnsSelection = QRadioButton()
self.showHymnsSelection.setChecked(False)
self.showHymnsSelection.clicked.connect(
lambda: self.selectRadio("hymns"))
layout1.addRow("Hymns", self.showHymnsSelection)
# Second column
layout2 = QVBoxLayout()
self.bibleWidget = QWidget()
self.bibleLayout = QFormLayout()
checkbox = QCheckBox()
checkbox.setText("")
checkbox.setChecked(config.presentationParser)
checkbox.stateChanged.connect(self.presentationParserChanged)
checkbox.setToolTip("Parse bible verse reference in the entered text")
self.bibleLayout.addRow("Bible Reference", checkbox)
versionCombo = QComboBox()
self.bibleVersions = self.parent.textList
versionCombo.addItems(self.bibleVersions)
initialIndex = 0
if config.mainText in self.bibleVersions:
initialIndex = self.bibleVersions.index(config.mainText)
versionCombo.setCurrentIndex(initialIndex)
versionCombo.currentIndexChanged.connect(self.changeBibleVersion)
self.bibleLayout.addRow("Bible Version", versionCombo)
self.textEntry = QPlainTextEdit("John 3:16; Rm 5:8")
self.bibleLayout.addRow(self.textEntry)
button = QPushButton("Presentation")
button.setToolTip("Go to Presentation")
button.clicked.connect(self.goToPresentation)
self.bibleLayout.addWidget(button)
self.bibleLayout.addItem(
QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding))
self.bibleWidget.setLayout(self.bibleLayout)
self.hymnWidget = QWidget()
self.hymnLayout = QFormLayout()
selected = 0
book = "Hymn Lyrics - English"
if book in self.books:
selected = self.books.index(book)
self.bookList = QComboBox()
self.bookList.addItems(self.books)
self.bookList.setCurrentIndex(selected)
self.bookList.currentIndexChanged.connect(self.selectHymnBook)
self.hymnLayout.addWidget(self.bookList)
self.chapterlist = QListView()
self.chapterlist.clicked.connect(self.selectHymn)
# self.chapterlist.selectionModel().selectionChanged.connect(self.selectHymn)
self.hymnLayout.addWidget(self.chapterlist)
self.buttons = []
for count in range(0, 10):
hymnButton = QPushButton()
hymnButton.setText(" ")
hymnButton.setEnabled(False)
hymnButton.clicked.connect(partial(self.selectParagraph, count))
self.hymnLayout.addWidget(hymnButton)
self.buttons.append(hymnButton)
self.selectHymnBook(selected)
self.hymnWidget.setLayout(self.hymnLayout)
self.hymnWidget.hide()
layout2.addWidget(self.bibleWidget)
if len(self.books) > 0:
layout2.addWidget(self.hymnWidget)
layout.addLayout(layout1)
layout.addLayout(layout2)
self.setLayout(layout)
def focusOutEvent(self, event):
# set up signals
self.userFinishedEditing()
return QPlainTextEdit.focusOutEvent(self, event)
def focusInEvent(self, event):
self.setOrigValue(self.text())
return QPlainTextEdit.focusInEvent(self, event)
def focusOutEvent(self, event):
"""Reimplemented to handle focus"""
self.focus_changed.emit()
QPlainTextEdit.focusOutEvent(self, event)
class ZusatzFensterKerndaten(QWidget):
def __init__(self, nummer, text):
super().__init__()
self.initMe(nummer, text)
def initMe(self, nummer, text):
self.l1 = QLabel(self)
self.l1.setText('Inhalt der eingelesenen Zelle')
self.l1.move(20, 5)
self.nummer = nummer
self.setGeometry(400, 300, 500, 700)
self.zelle = QPlainTextEdit(self)
self.zelle.setGeometry(0, 40, 500, 250)
self.zelle.setPlainText(text)
self.zelle.setReadOnly(True)
self.l2 = QLabel(self)
self.l2.setText(
"""Bitte geben Sie hier den Wert ein nach dem in der Zelle gesucht werden soll.
Bsp. Wollen Sie einen Lastpunkt auslesen, welcher mit 5000 rpm angegeben ist, geben Sie 5000 ein.
Achtung: keine Einheiten mit angeben. Nur Zahlen!""")
self.l2.move(10, 330)
self.eing = QLineEdit(self)
self.eing.move(10, 410)
p = QPushButton('Prüfen', self)
p.clicked.connect(self.pruefen)
p.move(180, 409)
self.l3 = QLabel(self)
self.l3.setText('vorangehende Zeichenkette')
self.l3.move(10, 460)
self.suchstring = QLineEdit(self)
self.suchstring.move(180, 459)
self.suchstring.setDisabled(True)
self.l5 = QLabel(self)
self.l5.setStyleSheet("background-color: yellow")
self.l5.setText(
"Prüfen Sie die vorrangehende Zeichenkette.\nSollte diese nicht stimmen, können Sie selbst eine angeben und erneut prüfen.\nAchtung: Leerzeichen nicht vergessen "
)
self.l5.move(10, 490)
self.l5.setVisible(False)
self.l4 = QLabel(self)
self.l4.setText('gefundener Eintrag')
self.l4.move(10, 540)
self.gefundener_string = QLineEdit(self)
self.gefundener_string.move(180, 539)
self.gefundener_string.setReadOnly(True)
frage = QPushButton(self)
frage.setIcon(QIcon("bilder_vorlagenersteller\\FrageIcon.png"))
frage.move(450, 10)
frage.clicked.connect(self.Hilfe)
self.weiter = QPushButton('Weiter', self)
self.weiter.move(420, 650)
self.weiter.setDisabled(True)
self.weiter.clicked.connect(self.weiter_gehts)
def suchstring_finden(self):
startindex = self.zelle.toPlainText().find(self.eing.text())
if startindex == 0:
suchstring = '##Anfang###'
elif startindex == -1:
suchstring = 'ungültige Eingabe'
else:
suchstring = ''
for i in range(0, 11):
suchstring = self.zelle.toPlainText()[startindex -
i] + suchstring
if (startindex - i) == 0:
break
return suchstring[:-1]
def pruefen(self):
suchstring = self.suchstring.text()
if suchstring == '':
suchstring = self.suchstring_finden()
print(suchstring)
self.suchstring.setDisabled(False)
self.l5.setVisible(True)
self.weiter.setDisabled(False)
self.suchstring.setText(suchstring)
startindex = self.zelle.toPlainText().find(suchstring) + len(
suchstring)
ende = startindex + len(self.eing.text())
self.gefundener_string.setText(
self.zelle.toPlainText()[startindex:ende])
def weiter_gehts(self):
w.findChild(QLabel, self.nummer).setVisible(True)
w.findChild(QLineEdit, 'suchstr' + self.nummer).setVisible(True)
w.findChild(QLineEdit,
'suchstr' + self.nummer).setText(self.suchstring.text())
self.close()
def Hilfe(self):
self.h = HilfeFenster(
"bilder_vorlagenersteller\\erweitertes_einlesen.png")
self.h.show()
class ArbeitsdatenFenster(QWidget):
def __init__(self):
super().__init__()
self.initMe()
def initMe(self):
kd = QLabel(self)
kd.setText(
'Einlesen der Arbeitsdaten\n\nMappe\t\t Zeile1 Spalte1 Länge Breite'
)
kd.move(100, 80)
dt = QLabel(self)
dt.setText(
'Gesamtmoment\n\n\n\n\n\n\n\n\nRadialkraft\n\n\n\n\n\n\n\n\nTangentialkraft\n\n\n\n\n\n\n\n\nBiegemoment'
)
dt.move(10, 133)
vb = QLabel(self)
vb.move(200, 110)
frage = QPushButton(self)
frage.setIcon(QIcon("bilder_vorlagenersteller\\FrageIcon.png"))
frage.move(510, 30)
frage.clicked.connect(self.Hilfe)
self.weiter = QPushButton('Weiter', self)
self.weiter.setDisabled(True)
self.weiter_gehts = [False, False, False, False]
self.weiter.move(480, 650)
self.weiter.clicked.connect(self.weiter_funkt)
name_dbox = [
'Dropbox\nGesamtmoment', 'Dropbox\nRadialkraft',
'Dropbox\nTangentialkraft', 'Dropbox\nBiegemoment'
]
for zeile in range(0, 4):
self.drop = Dropbox(self)
self.drop.setGeometry(420, 125 + zeile * 120, 140, 100)
self.drop.setText(name_dbox[zeile])
self.drop.setObjectName('Adrop' + str(zeile))
for spalte in range(0, 5):
self.eing = QPlainTextEdit(self)
self.eing.setAcceptDrops(False)
self.eing.setObjectName(str(zeile) + str(spalte))
self.eing.textChanged.connect(self.freigabe)
if spalte == 0:
self.eing.setGeometry(100 + 80 * spalte, 125 + zeile * 120,
80, 100)
elif spalte < 3:
self.eing.setGeometry(200 + 45 * (spalte - 1),
125 + zeile * 120, 40, 100)
else:
self.eing.setGeometry(210 + 45 * (spalte - 1),
125 + zeile * 120, 40, 100)
self.eing.textChanged.connect(self.freigabe)
self.show()
def freigabe(self):
self.weiter.setEnabled(True)
for zeile in range(0, 4):
for spalte in range(0, 5):
if self.findChild(QPlainTextEdit,
str(zeile) +
str(spalte)).toPlainText() == '':
self.weiter.setDisabled(True)
def weiter_funkt(self):
self.arbeits_daten = {}
datenblock = []
for zeile in range(0, 4):
datenzeile = []
for spalte in range(0, 5):
eintraege = self.findChild(QPlainTextEdit,
str(zeile) +
str(spalte)).toPlainText()
datenzeile.append(eintraege.split('\n'))
datenblock.append(datenzeile)
self.arbeits_daten['gesamt_moment'] = datenblock[0]
self.arbeits_daten['f_rad'] = datenblock[1]
self.arbeits_daten['f_tan'] = datenblock[2]
self.arbeits_daten['biege_moment'] = datenblock[3]
self.close()
def Hilfe(self):
self.h = HilfeFenster(
"bilder_vorlagenersteller\\einlesen_arbeitsdaten.png")
self.h.show()
def resizeEvent(self, *e):
cr = self.contentsRect()
rec = QRect(cr.left(), cr.top(), self.margin.getWidth(), cr.height())
self.margin.setGeometry(rec)
QPlainTextEdit.resizeEvent(self, *e)
class GetValueDialog(QDialog):
"""
A dialog that gets a single value
"""
def __init__(self, parent=None, label_name=''):
"""
:param parent:
:param label_name
"""
super(GetValueDialog, self).__init__(parent)
layout = QVBoxLayout(self)
# details information
self.info_line = QPlainTextEdit(self)
self.info_line.setEnabled(False)
layout.addWidget(self.info_line)
# input
self.label = QLabel(self)
self.value_edit = QLineEdit(self)
layout.addWidget(self.label)
layout.addWidget(self.value_edit)
# END-IF-ELSE
# nice widget for editing the date
# self.datetime = QDateTimeEdit(self)
# self.datetime.setCalendarPopup(True)
# self.datetime.setDateTime(QDateTime.currentDateTime())
# layout.addWidget(self.datetime)
# OK and Cancel buttons
buttons = QDialogButtonBox(QDialogButtonBox.Ok | QDialogButtonBox.Cancel,
QtCore.Qt.Horizontal, self)
buttons.accepted.connect(self.accept)
buttons.rejected.connect(self.reject)
layout.addWidget(buttons)
# set some values
self.setWindowTitle('Get user input')
self.label.setText(label_name)
return
# get current date and time from the dialog
def get_value(self):
""" get the value in string
:return:
"""
return str(self.value_edit.text())
def set_message_type(self, message_type):
"""
:param message_type:
:return:
"""
if message_type == 'error':
self.value_edit.setStyleSheet("color: rgb(255, 0, 0);")
else:
self.value_edit.setStyleSheet('color: blue')
return
def set_title(self, title):
"""
set window/dialog title
:param title:
:return:
"""
self.setWindowTitle(title)
return
def show_message(self, message):
"""
set or show message
:param message:
:return:
"""
self.info_line.setPlainText(message)
return
def render_data(self,
row,
spec1d_data=None,
spec2d_data=None,
image_data=None):
"""
Render the updated data sets in the individual plot widgets within the
MOSViz viewer.
"""
self._check_unsaved_comments()
if spec1d_data is not None:
spectrum1d_x = spec1d_data[spec1d_data.id['Wavelength']]
spectrum1d_y = spec1d_data[spec1d_data.id['Flux']]
spectrum1d_yerr = spec1d_data[spec1d_data.id['Uncertainty']]
self.spectrum1d_widget.set_data(x=spectrum1d_x,
y=spectrum1d_y,
yerr=spectrum1d_yerr)
# Try to retrieve the wcs information
try:
flux_unit = spec1d_data.header.get('BUNIT', 'Jy').lower()
flux_unit = flux_unit.replace('counts', 'count')
flux_unit = u.Unit(flux_unit)
except ValueError:
flux_unit = u.Unit("Jy")
try:
disp_unit = spec1d_data.header.get('CUNIT1',
'Angstrom').lower()
disp_unit = u.Unit(disp_unit)
except ValueError:
disp_unit = u.Unit("Angstrom")
self.spectrum1d_widget.axes.set_xlabel(
"Wavelength [{}]".format(disp_unit))
self.spectrum1d_widget.axes.set_ylabel(
"Flux [{}]".format(flux_unit))
if image_data is not None:
wcs = image_data.coords.wcs
self.image_widget.set_image(image_data.get_component(
image_data.id['Flux']).data,
wcs=wcs,
interpolation='none',
origin='lower')
self.image_widget.axes.set_xlabel("Spatial X")
self.image_widget.axes.set_ylabel("Spatial Y")
# Add the slit patch to the plot
ra = row[self.catalog.meta["special_columns"]
["slit_ra"]] * u.degree
dec = row[self.catalog.meta["special_columns"]
["slit_dec"]] * u.degree
slit_width = row[self.catalog.meta["special_columns"]
["slit_width"]]
slit_length = row[self.catalog.meta["special_columns"]
["slit_length"]]
skycoord = SkyCoord(ra, dec, frame='fk5')
xp, yp = skycoord.to_pixel(wcs)
scale = np.sqrt(proj_plane_pixel_area(wcs)) * 3600.
dx = slit_width / scale
dy = slit_length / scale
self.image_widget.draw_rectangle(x=xp, y=yp, width=dx, height=dy)
self.image_widget._redraw()
else:
self.image_widget.setVisible(False)
# Plot the 2D spectrum data last because by then we can make sure that
# we set up the extent of the image appropriately if the cutout and the
# 1D spectrum are present so that the axes can be locked.
if spec2d_data is not None:
wcs = spec2d_data.coords.wcs
xp2d = np.arange(spec2d_data.shape[1])
yp2d = np.repeat(0, spec2d_data.shape[1])
spectrum2d_disp, spectrum2d_offset = spec2d_data.coords.pixel2world(
xp2d, yp2d)
x_min = spectrum2d_disp.min()
x_max = spectrum2d_disp.max()
if image_data is None:
y_min = -0.5
y_max = spec2d_data.shape[0] - 0.5
else:
y_min = yp - dy / 2.
y_max = yp + dy / 2.
extent = [x_min, x_max, y_min, y_max]
self.spectrum2d_widget.set_image(image=spec2d_data.get_component(
spec2d_data.id['Flux']).data,
interpolation='none',
aspect='auto',
extent=extent,
origin='lower')
self.spectrum2d_widget.axes.set_xlabel("Wavelength")
self.spectrum2d_widget.axes.set_ylabel("Spatial Y")
self.spectrum2d_widget._redraw()
# Clear the meta information widget
# NOTE: this process is inefficient
for i in range(self.meta_form_layout.count()):
wid = self.meta_form_layout.itemAt(i).widget()
label = self.meta_form_layout.labelForField(wid)
if label is not None:
label.deleteLater()
wid.deleteLater()
# Repopulate the form layout
# NOTE: this process is inefficient
for col in row.colnames:
if col.lower() not in ["comments", "flag"]:
line_edit = QLineEdit(str(row[col]),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow(col, line_edit)
# Set up comment and flag input/display boxes
if self.comments:
if self.savepath is not None:
if self.savepath == -1:
line_edit = QLineEdit(
os.path.basename("Not Saving to File."),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
else:
line_edit = QLineEdit(os.path.basename(self.savepath),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
self.input_flag = QLineEdit(self.get_flag(),
self.central_widget.meta_form_widget)
self.input_flag.textChanged.connect(self._text_changed)
self.input_flag.setStyleSheet(
"background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Flag", self.input_flag)
self.input_comments = QPlainTextEdit(
self.get_comment(), self.central_widget.meta_form_widget)
self.input_comments.textChanged.connect(self._text_changed)
self.input_comments.setStyleSheet(
"background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Comments", self.input_comments)
self.input_save = QPushButton('Save',
self.central_widget.meta_form_widget)
self.input_save.clicked.connect(self.update_comments)
self.input_save.setDefault(True)
self.input_refresh = QPushButton(
'Reload', self.central_widget.meta_form_widget)
self.input_refresh.clicked.connect(self.refresh_comments)
self.meta_form_layout.addRow(self.input_save, self.input_refresh)
def __initWidgets(self):
self.consoleEdit = QPlainTextEdit()
self.setWidget(self.consoleEdit)
def focusInEvent(self, event):
"""Reimplemented to handle focus"""
self.focus_changed.emit()
self.focus_in.emit()
self.highlight_current_cell()
QPlainTextEdit.focusInEvent(self, event)
def render_data(self,
row,
spec1d_data=None,
spec2d_data=None,
image_data=None,
level2_data=None):
"""
Render the updated data sets in the individual plot widgets within the
MOSViz viewer.
"""
self._check_unsaved_comments()
self.image_viewer_hidden = image_data is None
if spec1d_data is not None:
# TODO: This should not be needed. Must explore why the core model
# is out of sync with the proxy model.
self.spectrum1d_widget.plot_widget.clear_plots()
# Clear the specviz model of any rendered plot items
self._specviz_viewer.model.clear()
# Create a new Spectrum1D object from the flux data attribute of
# the incoming data
spec = glue_data_to_spectrum1d(spec1d_data, 'Flux')
# Create a DataItem from the Spectrum1D object, which adds the data
# to the internel specviz model
data_item = self._specviz_viewer.model.add_data(spec, 'Spectrum1D')
# Get the PlotDataItem rendered via the plot's proxy model and
# ensure that it is visible in the plot
plot_data_item = self.spectrum1d_widget.proxy_model.item_from_id(
data_item.identifier)
plot_data_item.visible = True
plot_data_item.color = "#000000"
# Explicitly let the plot widget know that data items have changed
self.spectrum1d_widget.plot_widget.on_item_changed(data_item)
if not self.image_viewer_hidden:
if not self.image_widget.isVisible():
self.image_widget.setVisible(True)
wcs = image_data.coords.wcs
self.cutout_wcs = wcs
array = image_data.get_component(image_data.id['Flux']).data
# Add the slit patch to the plot
self.slit_controller.clear_slits()
if "slit_width" in self.catalog.meta["special_columns"] and \
"slit_length" in self.catalog.meta["special_columns"] and \
wcs is not None:
self.add_slit(row)
self.image_widget.draw_slit()
else:
self.image_widget.reset_limits()
self.image_widget.set_image(array,
wcs=wcs,
interpolation='none',
origin='lower')
self.image_widget.axes.set_xlabel("Spatial X")
self.image_widget.axes.set_ylabel("Spatial Y")
if self.slit_controller.has_slits:
self.image_widget.set_slit_limits()
self.image_widget._redraw()
else:
self.cutout_wcs = None
# Plot the 2D spectrum data last because by then we can make sure that
# we set up the extent of the image appropriately if the cutout and the
# 1D spectrum are present so that the axes can be locked.
# We are repurposing the spectrum 2d widget to handle the display of both
# the level 3 and level 2 spectra.
if spec2d_data is not None or level2_data is not None:
self._load_spectrum2d_widget(spec2d_data, level2_data)
else:
self.spectrum2d_widget.no_data()
# Clear the meta information widget
# NOTE: this process is inefficient
for i in range(self.meta_form_layout.count()):
wid = self.meta_form_layout.itemAt(i).widget()
label = self.meta_form_layout.labelForField(wid)
if label is not None:
label.deleteLater()
wid.deleteLater()
# Repopulate the form layout
# NOTE: this process is inefficient
for col in row.colnames:
if col.lower() not in ["comments", "flag"]:
line_edit = QLineEdit(str(row[col]),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow(col, line_edit)
# Set up comment and flag input/display boxes
if self.comments:
if self.savepath is not None:
if self.savepath == -1:
line_edit = QLineEdit(
os.path.basename("Not Saving to File."),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
else:
line_edit = QLineEdit(os.path.basename(self.savepath),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
self.input_flag = QLineEdit(self.get_flag(),
self.central_widget.meta_form_widget)
self.input_flag.textChanged.connect(self._text_changed)
self.input_flag.setStyleSheet(
"background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Flag", self.input_flag)
self.input_comments = QPlainTextEdit(
self.get_comment(), self.central_widget.meta_form_widget)
self.input_comments.textChanged.connect(self._text_changed)
self.input_comments.setStyleSheet(
"background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Comments", self.input_comments)
self.input_save = QPushButton('Save',
self.central_widget.meta_form_widget)
self.input_save.clicked.connect(self.update_comments)
self.input_save.setDefault(True)
self.input_refresh = QPushButton(
'Reload', self.central_widget.meta_form_widget)
self.input_refresh.clicked.connect(self.refresh_comments)
self.meta_form_layout.addRow(self.input_save, self.input_refresh)
if not self.isHidden() and self.image_viewer_hidden:
self.image_widget.setVisible(False)
class Properties(QWidget):
def __init__(self, settings: PartSettings):
super().__init__()
self._settings = settings
self.export_btn = QPushButton("Export profile")
self.export_btn.clicked.connect(self.export_profile)
self.import_btn = QPushButton("Import profile")
self.import_btn.clicked.connect(self.import_profiles)
self.export_pipeline_btn = QPushButton("Export pipeline")
self.export_pipeline_btn.clicked.connect(self.export_pipeline)
self.import_pipeline_btn = QPushButton("Import pipeline")
self.import_pipeline_btn.clicked.connect(self.import_pipeline)
self.delete_btn = QPushButton("Delete profile")
self.delete_btn.setDisabled(True)
self.delete_btn.clicked.connect(self.delete_profile)
self.multiple_files_chk = QCheckBox("Show multiple files panel")
self.multiple_files_chk.setChecked(
self._settings.get("multiple_files_widget", False))
self.multiple_files_chk.stateChanged.connect(
self.multiple_files_visibility)
self.rename_btn = QPushButton("Rename profile")
self.rename_btn.clicked.connect(self.rename_profile)
self.rename_btn.setDisabled(True)
self.voxel_size_label = QLabel()
self.info_label = QPlainTextEdit()
self.info_label.setReadOnly(True)
self.profile_list = SearchableListWidget()
self.profile_list.currentTextChanged.connect(self.profile_chosen)
self.pipeline_list = SearchableListWidget()
self.pipeline_list.currentTextChanged.connect(self.profile_chosen)
self.spacing = [QDoubleSpinBox() for _ in range(3)]
self.lock_spacing = LockCheckBox()
self.lock_spacing.stateChanged.connect(self.spacing[1].setDisabled)
self.lock_spacing.stateChanged.connect(self.synchronize_spacing)
# noinspection PyUnresolvedReferences
self.spacing[2].valueChanged.connect(self.synchronize_spacing)
units_value = self._settings.get("units_value", Units.nm)
for el in self.spacing:
el.setAlignment(Qt.AlignRight)
el.setButtonSymbols(QAbstractSpinBox.NoButtons)
el.setRange(0, 1000000)
# noinspection PyUnresolvedReferences
el.valueChanged.connect(self.image_spacing_change)
self.units = EnumComboBox(Units)
self.units.set_value(units_value)
# noinspection PyUnresolvedReferences
self.units.currentIndexChanged.connect(self.update_spacing)
spacing_layout = QHBoxLayout()
spacing_layout.addWidget(self.lock_spacing)
for txt, el in zip(["x", "y", "z"], self.spacing[::-1]):
spacing_layout.addWidget(QLabel(txt + ":"))
spacing_layout.addWidget(el)
spacing_layout.addWidget(self.units)
spacing_layout.addStretch(1)
voxel_size_layout = QHBoxLayout()
voxel_size_layout.addWidget(self.voxel_size_label)
voxel_size_layout.addSpacing(30)
profile_layout = QGridLayout()
profile_layout.setSpacing(0)
profile_layout.addWidget(QLabel("Profiles:"), 0, 0)
profile_layout.addWidget(self.profile_list, 1, 0)
profile_layout.addWidget(QLabel("Pipelines:"), 2, 0)
profile_layout.addWidget(self.pipeline_list, 3, 0, 4, 1)
profile_layout.addWidget(self.info_label, 1, 1, 3, 2)
profile_layout.addWidget(self.export_btn, 4, 1)
profile_layout.addWidget(self.import_btn, 4, 2)
profile_layout.addWidget(self.export_pipeline_btn, 5, 1)
profile_layout.addWidget(self.import_pipeline_btn, 5, 2)
profile_layout.addWidget(self.delete_btn, 6, 1)
profile_layout.addWidget(self.rename_btn, 6, 2)
layout = QVBoxLayout()
layout.addLayout(spacing_layout)
layout.addLayout(voxel_size_layout)
layout.addWidget(self.multiple_files_chk)
layout.addLayout(profile_layout, 1)
self.setLayout(layout)
@Slot(int)
def multiple_files_visibility(self, val: int):
self._settings.set("multiple_files_widget", val)
# @Slot(str) # PySide bug
def profile_chosen(self, text):
if text == "":
self.delete_btn.setEnabled(False)
self.rename_btn.setEnabled(False)
self.info_label.setPlainText("")
return
try:
if self.sender() == self.profile_list.list_widget:
profile = self._settings.segmentation_profiles[text]
self.pipeline_list.selectionModel().clear()
self.delete_btn.setText("Delete profile")
self.rename_btn.setText("Rename profile")
elif self.sender() == self.pipeline_list.list_widget:
profile = self._settings.segmentation_pipelines[text]
self.profile_list.selectionModel().clear()
self.delete_btn.setText("Delete pipeline")
self.rename_btn.setText("Rename pipeline")
else:
return
except KeyError:
return
# TODO update with knowledge from profile dict
self.delete_btn.setEnabled(True)
self.rename_btn.setEnabled(True)
self.info_label.setPlainText(
profile.pretty_print(analysis_algorithm_dict))
def synchronize_spacing(self):
if self.lock_spacing.isChecked():
self.spacing[1].setValue(self.spacing[2].value())
def image_spacing_change(self):
spacing = [
el.value() / UNIT_SCALE[self.units.currentIndex()]
for i, el in enumerate(self.spacing)
]
if not self.spacing[0].isEnabled():
spacing = spacing[1:]
self._settings.image_spacing = spacing
voxel_size = 1
for el in self._settings.image_spacing:
voxel_size *= el * UNIT_SCALE[self.units.currentIndex()]
self.voxel_size_label.setText(
f"Voxel_size: {voxel_size} {self.units.get_value().name}"
f"<sup>{len(self._settings.image_spacing)}</sup>")
def update_spacing(self, index=None):
voxel_size = 1
value = self.units.get_value()
if index is not None:
self._settings.set("units_value", value)
for el, sp in zip(self.spacing[::-1],
self._settings.image_spacing[::-1]):
el.blockSignals(True)
current_size = sp * UNIT_SCALE[self.units.currentIndex()]
voxel_size *= current_size
el.setValue(current_size)
el.blockSignals(False)
self.spacing[0].setDisabled(len(self._settings.image_spacing) == 2)
self.voxel_size_label.setText(
f"Voxel_size: {voxel_size} {value.name}"
f"<sup>{len(self._settings.image_spacing)}</sup>")
def update_profile_list(self):
current_names = set(self._settings.segmentation_profiles.keys())
self.profile_list.clear()
self.profile_list.addItems(sorted(current_names))
self.pipeline_list.clear()
self.pipeline_list.addItems(
sorted(set(self._settings.segmentation_pipelines.keys())))
self.delete_btn.setDisabled(True)
self.rename_btn.setDisabled(True)
self.info_label.setPlainText("")
def showEvent(self, _event):
self.update_profile_list()
self.update_spacing()
def event(self, event: QEvent):
if event.type() == QEvent.WindowActivate and self.isVisible():
self.update_profile_list()
self.update_spacing()
self.multiple_files_chk.setChecked(
self._settings.get("multiple_files_widget", False))
return super().event(event)
def delete_profile(self):
text, dkt = "", {}
if self.profile_list.selectedItems():
text = self.profile_list.selectedItems()[0].text()
dkt = self._settings.segmentation_profiles
elif self.pipeline_list.selectedItems():
text = self.pipeline_list.selectedItems()[0].text()
dkt = self._settings.segmentation_pipelines
if text != "":
self.delete_btn.setDisabled(True)
del dkt[text]
self.update_profile_list()
def export_profile(self):
exp = ExportDialog(self._settings.segmentation_profiles,
ProfileDictViewer)
if not exp.exec_():
return
dial = QFileDialog(self, "Export profile segment")
dial.setFileMode(QFileDialog.AnyFile)
dial.setAcceptMode(QFileDialog.AcceptSave)
dial.setDirectory(
self._settings.get("io.save_directory", str(Path.home())))
dial.setNameFilter("Segment profile (*.json)")
dial.setDefaultSuffix("json")
dial.selectFile("segment_profile.json")
dial.setHistory(dial.history() + self._settings.get_path_history())
if dial.exec_():
file_path = dial.selectedFiles()[0]
self._settings.set("io.save_directory", os.path.dirname(file_path))
self._settings.add_path_history(os.path.dirname(file_path))
data = {
x: self._settings.segmentation_profiles[x]
for x in exp.get_export_list()
}
with open(file_path, "w") as ff:
json.dump(data,
ff,
cls=self._settings.json_encoder_class,
indent=2)
def import_profiles(self):
dial = QFileDialog(self, "Import profile segment")
dial.setFileMode(QFileDialog.ExistingFile)
dial.setAcceptMode(QFileDialog.AcceptOpen)
dial.setDirectory(
self._settings.get("io.save_directory", str(Path.home())))
dial.setNameFilter("Segment profile (*.json)")
dial.setHistory(dial.history() + self._settings.get_path_history())
if dial.exec_():
file_path = dial.selectedFiles()[0]
save_dir = os.path.dirname(file_path)
self._settings.set("io.save_directory", save_dir)
self._settings.add_path_history(save_dir)
profs, err = self._settings.load_part(file_path)
if err:
QMessageBox.warning(
self, "Import error",
"error during importing, part of data were filtered.")
profiles_dict = self._settings.segmentation_profiles
imp = ImportDialog(profs, profiles_dict, ProfileDictViewer)
if not imp.exec_():
return
for original_name, final_name in imp.get_import_list():
profiles_dict[final_name] = profs[original_name]
self._settings.dump()
self.update_profile_list()
def export_pipeline(self):
exp = ExportDialog(self._settings.segmentation_pipelines,
ProfileDictViewer)
if not exp.exec_():
return
dial = QFileDialog(self, "Export pipeline segment")
dial.setFileMode(QFileDialog.AnyFile)
dial.setAcceptMode(QFileDialog.AcceptSave)
dial.setDirectory(self._settings.get("io.save_directory", ""))
dial.setNameFilter("Segment pipeline (*.json)")
dial.setDefaultSuffix("json")
dial.selectFile("segment_pipeline.json")
dial.setHistory(dial.history() + self._settings.get_path_history())
if dial.exec_():
file_path = dial.selectedFiles()[0]
data = {
x: self._settings.segmentation_pipelines[x]
for x in exp.get_export_list()
}
with open(file_path, "w") as ff:
json.dump(data,
ff,
cls=self._settings.json_encoder_class,
indent=2)
self._settings.set("io.save_directory", os.path.dirname(file_path))
self._settings.add_path_history(os.path.dirname(file_path))
def import_pipeline(self):
dial = QFileDialog(self, "Import pipeline segment")
dial.setFileMode(QFileDialog.ExistingFile)
dial.setAcceptMode(QFileDialog.AcceptOpen)
dial.setDirectory(self._settings.get("io.save_directory", ""))
dial.setNameFilter("Segment pipeline (*.json)")
dial.setHistory(dial.history() + self._settings.get_path_history())
if dial.exec_():
file_path = dial.selectedFiles()[0]
self._settings.set("io.save_directory", os.path.dirname(file_path))
self._settings.add_path_history(os.path.dirname(file_path))
profs, err = self._settings.load_part(file_path)
if err:
QMessageBox.warning(
self, "Import error",
"error during importing, part of data were filtered.")
profiles_dict = self._settings.segmentation_pipelines
imp = ImportDialog(profs, profiles_dict, ProfileDictViewer)
if not imp.exec_():
return
for original_name, final_name in imp.get_import_list():
profiles_dict[final_name] = profs[original_name]
self._settings.dump()
self.update_profile_list()
def rename_profile(self):
profile_name, profiles_dict = "", {}
if self.profile_list.selectedItems():
profile_name = self.profile_list.selectedItems()[0].text()
profiles_dict = self._settings.segmentation_profiles
elif self.pipeline_list.selectedItems():
profile_name = self.pipeline_list.selectedItems()[0].text()
profiles_dict = self._settings.segmentation_pipelines
if profile_name == "":
return
text, ok = QInputDialog.getText(self,
"New profile name",
f"New name for {profile_name}",
text=profile_name)
if ok:
text = text.strip()
if text in profiles_dict.keys():
res = QMessageBox.warning(
self,
"Already exist",
f"Profile with name {text} already exist. Would you like to overwrite?",
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No,
)
if res == QMessageBox.No:
self.rename_profile()
return
profiles_dict[text] = profiles_dict.pop(profile_name)
self._settings.dump()
self.update_profile_list()
def render_data(self, row, spec1d_data=None, spec2d_data=None,
image_data=None, level2_data=None):
"""
Render the updated data sets in the individual plot widgets within the
MOSViz viewer.
"""
self._check_unsaved_comments()
self.image_viewer_hidden = image_data is None
if spec1d_data is not None:
# TODO: This should not be needed. Must explore why the core model
# is out of sync with the proxy model.
self.spectrum1d_widget.plot_widget.clear_plots()
# Clear the specviz model of any rendered plot items
self._specviz_viewer.model.clear()
# Create a new Spectrum1D object from the flux data attribute of
# the incoming data
spec = glue_data_to_spectrum1d(spec1d_data, 'Flux')
# Create a DataItem from the Spectrum1D object, which adds the data
# to the internel specviz model
data_item = self._specviz_viewer.model.add_data(spec, 'Spectrum1D')
# Get the PlotDataItem rendered via the plot's proxy model and
# ensure that it is visible in the plot
plot_data_item = self.spectrum1d_widget.proxy_model.item_from_id(data_item.identifier)
plot_data_item.visible = True
plot_data_item.color = "#000000"
# Explicitly let the plot widget know that data items have changed
self.spectrum1d_widget.plot_widget.on_item_changed(data_item)
if not self.image_viewer_hidden:
if not self.image_widget.isVisible():
self.image_widget.setVisible(True)
wcs = image_data.coords.wcs
self.cutout_wcs = wcs
array = image_data.get_component(image_data.id['Flux']).data
# Add the slit patch to the plot
self.slit_controller.clear_slits()
if "slit_width" in self.catalog.meta["special_columns"] and \
"slit_length" in self.catalog.meta["special_columns"] and \
wcs is not None:
self.add_slit(row)
self.image_widget.draw_slit()
else:
self.image_widget.reset_limits()
self.image_widget.set_image(array, wcs=wcs, interpolation='none', origin='lower')
self.image_widget.axes.set_xlabel("Spatial X")
self.image_widget.axes.set_ylabel("Spatial Y")
if self.slit_controller.has_slits:
self.image_widget.set_slit_limits()
self.image_widget._redraw()
else:
self.cutout_wcs = None
# Plot the 2D spectrum data last because by then we can make sure that
# we set up the extent of the image appropriately if the cutout and the
# 1D spectrum are present so that the axes can be locked.
# We are repurposing the spectrum 2d widget to handle the display of both
# the level 3 and level 2 spectra.
if spec2d_data is not None or level2_data is not None:
self._load_spectrum2d_widget(spec2d_data, level2_data)
else:
self.spectrum2d_widget.no_data()
# Clear the meta information widget
# NOTE: this process is inefficient
for i in range(self.meta_form_layout.count()):
wid = self.meta_form_layout.itemAt(i).widget()
label = self.meta_form_layout.labelForField(wid)
if label is not None:
label.deleteLater()
wid.deleteLater()
# Repopulate the form layout
# NOTE: this process is inefficient
for col in row.colnames:
if col.lower() not in ["comments", "flag"]:
line_edit = QLineEdit(str(row[col]),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow(col, line_edit)
# Set up comment and flag input/display boxes
if self.comments:
if self.savepath is not None:
if self.savepath == -1:
line_edit = QLineEdit(os.path.basename("Not Saving to File."),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
else:
line_edit = QLineEdit(os.path.basename(self.savepath),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
self.input_flag = QLineEdit(self.get_flag(),
self.central_widget.meta_form_widget)
self.input_flag.textChanged.connect(self._text_changed)
self.input_flag.setStyleSheet("background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Flag", self.input_flag)
self.input_comments = QPlainTextEdit(self.get_comment(),
self.central_widget.meta_form_widget)
self.input_comments.textChanged.connect(self._text_changed)
self.input_comments.setStyleSheet("background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Comments", self.input_comments)
self.input_save = QPushButton('Save',
self.central_widget.meta_form_widget)
self.input_save.clicked.connect(self.update_comments)
self.input_save.setDefault(True)
self.input_refresh = QPushButton('Reload',
self.central_widget.meta_form_widget)
self.input_refresh.clicked.connect(self.refresh_comments)
self.meta_form_layout.addRow(self.input_save, self.input_refresh)
if not self.isHidden() and self.image_viewer_hidden:
self.image_widget.setVisible(False)
def __init__(self, parent=None):
QPlainTextEdit.__init__(self, parent)
BaseEditMixin.__init__(self)
self.setAttribute(Qt.WA_DeleteOnClose)
self.extra_selections_dict = {}
self._restore_selection_pos = None
# Trailing newlines/spaces trimming
self.remove_trailing_spaces = False
self.remove_trailing_newlines = False
# Add a new line when saving
self.add_newline = False
# Code snippets
self.code_snippets = True
self.textChanged.connect(self.changed)
self.cursorPositionChanged.connect(self.cursor_position_changed)
self.indent_chars = " " * 4
self.tab_stop_width_spaces = 4
# Code completion / calltips
if parent is not None:
mainwin = parent
while not isinstance(mainwin, QMainWindow):
mainwin = mainwin.parent()
if mainwin is None:
break
if mainwin is not None:
parent = mainwin
self.completion_widget = CompletionWidget(self, parent)
self.codecompletion_auto = False
self.setup_completion()
self.calltip_widget = CallTipWidget(self, hide_timer_on=False)
self.calltip_position = None
self.tooltip_widget = ToolTipWidget(self, as_tooltip=True)
self.highlight_current_cell_enabled = False
# The color values may be overridden by the syntax highlighter
# Highlight current line color
self.currentline_color = QColor(Qt.red).lighter(190)
self.currentcell_color = QColor(Qt.red).lighter(194)
# Brace matching
self.bracepos = None
self.matched_p_color = QColor(Qt.green)
self.unmatched_p_color = QColor(Qt.red)
self.decorations = TextDecorationsManager(self)
# Save current cell. This is invalidated as soon as the text changes.
# Useful to avoid recomputing while scrolling.
self.current_cell = None
def reset_current_cell():
self.current_cell = None
self.textChanged.connect(reset_current_cell)
class MOSVizViewer(DataViewer):
LABEL = "MOSViz Viewer"
window_closed = Signal()
_toolbar_cls = MOSViewerToolbar
def __init__(self, session, parent=None):
super(MOSVizViewer, self).__init__(session, parent=parent)
self.load_ui()
# Define some data containers
self.filepath = None
self.savepath = None
self.data_idx = None
self.comments = False
self.textChangedAt = None
self.mask = None
self.catalog = None
self.current_row = None
self._specviz_instance = None
self._loaded_data = {}
self._primary_data = None
self._layer_view = SimpleLayerWidget(parent=self)
self._layer_view.layer_combo.currentIndexChanged.connect(
self._selection_changed)
self.resize(800, 600)
def load_ui(self):
"""
Setup the MOSView viewer interface.
"""
self.central_widget = QWidget(self)
path = os.path.join(UI_DIR, 'mos_widget.ui')
loadUi(path, self.central_widget)
self.image_widget = DrawableImageWidget()
self.spectrum2d_widget = MOSImageWidget()
self.spectrum1d_widget = Line1DWidget()
# Set up helper for sharing axes. SharedAxisHelper defaults to no sharing
# and we control the sharing later by setting .sharex and .sharey on the
# helper
self.spectrum2d_spectrum1d_share = SharedAxisHelper(
self.spectrum2d_widget._axes, self.spectrum1d_widget._axes)
self.spectrum2d_image_share = SharedAxisHelper(
self.spectrum2d_widget._axes, self.image_widget._axes)
# We only need to set the image widget to keep the same aspect ratio
# since the two other viewers don't require square pixels, so the axes
# should not change shape.
self.image_widget._axes.set_adjustable('datalim')
self.meta_form_layout = self.central_widget.meta_form_layout
self.meta_form_layout.setFieldGrowthPolicy(
self.meta_form_layout.ExpandingFieldsGrow)
self.central_widget.left_vertical_splitter.insertWidget(
0, self.image_widget)
self.central_widget.right_vertical_splitter.addWidget(
self.spectrum2d_widget)
self.central_widget.right_vertical_splitter.addWidget(
self.spectrum1d_widget)
# Set the splitter stretch factors
self.central_widget.left_vertical_splitter.setStretchFactor(0, 1)
self.central_widget.left_vertical_splitter.setStretchFactor(1, 8)
self.central_widget.right_vertical_splitter.setStretchFactor(0, 1)
self.central_widget.right_vertical_splitter.setStretchFactor(1, 2)
self.central_widget.horizontal_splitter.setStretchFactor(0, 1)
self.central_widget.horizontal_splitter.setStretchFactor(1, 2)
# Keep the left and right splitters in sync otherwise the axes don't line up
self.central_widget.left_vertical_splitter.splitterMoved.connect(
self._left_splitter_moved)
self.central_widget.right_vertical_splitter.splitterMoved.connect(
self._right_splitter_moved)
# Set the central widget
self.setCentralWidget(self.central_widget)
# Define the options widget
self._options_widget = OptionsWidget()
def show(self, *args, **kwargs):
super(MOSVizViewer, self).show(*args, **kwargs)
# Trigger a sync between the splitters
self._left_splitter_moved()
@avoid_circular
def _right_splitter_moved(self, *args, **kwargs):
sizes = self.central_widget.right_vertical_splitter.sizes()
if sizes == [0, 0]:
sizes = [230, 230]
self.central_widget.left_vertical_splitter.setSizes(sizes)
@avoid_circular
def _left_splitter_moved(self, *args, **kwargs):
sizes = self.central_widget.left_vertical_splitter.sizes()
if sizes == [0, 0]:
sizes = [230, 230]
self.central_widget.right_vertical_splitter.setSizes(sizes)
def setup_connections(self):
"""
Connects gui elements to event calls.
"""
# Connect the selection event for the combo box to what's displayed
self.toolbar.source_select.currentIndexChanged[int].connect(
lambda ind: self.load_selection(self.catalog[ind]))
self.toolbar.source_select.currentIndexChanged[int].connect(
lambda ind: self._set_navigation(ind))
# Connect the specviz button
if SpecVizViewer is not None:
self.toolbar.open_specviz.triggered.connect(
lambda: self._open_in_specviz())
else:
self.toolbar.open_specviz.setDisabled(True)
# Connect previous and forward buttons
self.toolbar.cycle_next_action.triggered.connect(
lambda: self._set_navigation(self.toolbar.source_select.
currentIndex() + 1))
# Connect previous and previous buttons
self.toolbar.cycle_previous_action.triggered.connect(
lambda: self._set_navigation(self.toolbar.source_select.
currentIndex() - 1))
# Connect the toolbar axes setting actions
self.toolbar.lock_x_action.triggered.connect(
lambda state: self.set_locked_axes(x=state))
self.toolbar.lock_y_action.triggered.connect(
lambda state: self.set_locked_axes(y=state))
def options_widget(self):
return self._options_widget
def initialize_toolbar(self):
"""
Initialize the custom toolbar for the MOSViz viewer.
"""
from glue.config import viewer_tool
self.toolbar = self._toolbar_cls(self)
for tool_id in self.tools:
mode_cls = viewer_tool.members[tool_id]
mode = mode_cls(self)
self.toolbar.add_tool(mode)
self.addToolBar(self.toolbar)
self.setup_connections()
def register_to_hub(self, hub):
super(MOSVizViewer, self).register_to_hub(hub)
def has_data_or_subset(x):
if x.sender is self._primary_data:
return True
elif isinstance(x.sender,
Subset) and x.sender.data is self._primary_data:
return True
else:
return False
hub.subscribe(self,
msg.SubsetCreateMessage,
handler=self._add_subset,
filter=has_data_or_subset)
hub.subscribe(self,
msg.SubsetUpdateMessage,
handler=self._update_subset,
filter=has_data_or_subset)
hub.subscribe(self,
msg.SubsetDeleteMessage,
handler=self._remove_subset,
filter=has_data_or_subset)
hub.subscribe(self,
msg.DataUpdateMessage,
handler=self._update_data,
filter=has_data_or_subset)
def add_data(self, data):
"""
Processes data message from the central communication hub.
Parameters
----------
data : :class:`glue.core.data.Data`
Data object.
"""
# Check whether the data is suitable for the MOSViz viewer - basically
# we expect a table of 1D columns with at least three string and four
# floating-point columns.
if data.ndim != 1:
QMessageBox.critical(self,
"Error", "MOSViz viewer can only be used "
"for data with 1-dimensional components",
buttons=QMessageBox.Ok)
return False
components = [
data.get_component(cid) for cid in data.visible_components
]
categorical = [c for c in components if c.categorical]
if len(categorical) < 3:
QMessageBox.critical(
self,
"Error", "MOSViz viewer expected at least "
"three string components/columns, representing "
"the filenames of the 1D and 2D spectra and "
"cutouts",
buttons=QMessageBox.Ok)
return False
# We can relax the following requirement if we make the slit parameters
# optional
numerical = [c for c in components if c.numeric]
if len(numerical) < 4:
QMessageBox.critical(
self,
"Error", "MOSViz viewer expected at least "
"four numerical components/columns, representing "
"the slit position, length, and position angle",
buttons=QMessageBox.Ok)
return False
# Make sure the loaders and column names are correct
result = confirm_loaders_and_column_names(data)
if not result:
return False
self._primary_data = data
self._layer_view.data = data
self._unpack_selection(data)
return True
def add_subset(self, subset):
"""
Processes subset messages from the central communication hub.
Parameters
----------
subset :
Subset object.
"""
self._layer_view.refresh()
index = self._layer_view.layer_combo.findData(subset)
self._layer_view.layer_combo.setCurrentIndex(index)
return True
def _update_data(self, message):
"""
Update data message.
Parameters
----------
message : :class:`glue.core.message.Message`
Data message object.
"""
self._layer_view.refresh()
def _add_subset(self, message):
"""
Add subset message.
Parameters
----------
message : :class:`glue.core.message.Message`
Subset message object.
"""
self._layer_view.refresh()
def _update_subset(self, message):
"""
Update subset message.
Parameters
----------
message : :class:`glue.core.message.Message`
Update message object.
"""
self._layer_view.refresh()
self._unpack_selection(message.subset)
def _remove_subset(self, message):
"""
Remove subset message.
Parameters
----------
message : :class:`glue.core.message.Message`
Subset message object.
"""
self._layer_view.refresh()
self._unpack_selection(message.subset.data)
def _selection_changed(self):
self._unpack_selection(self._layer_view.layer_combo.currentData())
def _unpack_selection(self, data):
"""
Interprets the :class:`glue.core.data.Data` object by decomposing the
data elements, extracting relevant data, and recomposing a
package-agnostic dictionary object containing the relevant data.
Parameters
----------
data : :class:`glue.core.data.Data`
Glue data object to decompose.
"""
mask = None
if isinstance(data, Subset):
try:
mask = data.to_mask()
except IncompatibleAttribute:
return
if not np.any(mask):
return
data = data.data
self.mask = mask
# Clear the table
self.catalog = Table()
self.catalog.meta = data.meta
self.comments = False
col_names = data.components
for att in col_names:
cid = data.id[att]
component = data.get_component(cid)
if component.categorical:
comp_labels = component.labels[mask]
if comp_labels.ndim > 1:
comp_labels = comp_labels[0]
if str(att) in ["comments", "flag"]:
self.comments = True
elif str(att) in ['spectrum1d', 'spectrum2d', 'cutout']:
self.filepath = component._load_log.path
path = '/'.join(component._load_log.path.split('/')[:-1])
self.catalog[str(att)] = [
os.path.join(path, x) for x in comp_labels
]
else:
self.catalog[str(att)] = comp_labels
else:
comp_data = component.data[mask]
if comp_data.ndim > 1:
comp_data = comp_data[0]
self.catalog[str(att)] = comp_data
if len(self.catalog) > 0:
if not self.comments:
self.comments = self._load_comments(data.label) #Returns bool
else:
self._data_collection_index(data.label)
self._get_save_path()
# Update gui elements
self._update_navigation(select=0)
def _update_navigation(self, select=0):
"""
Updates the :class:`qtpy.QtWidgets.QComboBox` widget with the
appropriate source `id`s from the MOS catalog.
"""
if self.toolbar is None:
return
self.toolbar.source_select.blockSignals(True)
self.toolbar.source_select.clear()
if len(self.catalog) > 0 and self.catalog.meta["special_columns"][
"source_id"] in self.catalog.colnames:
self.toolbar.source_select.addItems(self.catalog[
self.catalog.meta["special_columns"]["source_id"]][:])
self.toolbar.source_select.setCurrentIndex(select)
self.toolbar.source_select.blockSignals(False)
self.toolbar.source_select.currentIndexChanged.emit(select)
def _set_navigation(self, index):
if len(self.catalog) < index:
return
if 0 <= index < self.toolbar.source_select.count():
self.toolbar.source_select.setCurrentIndex(index)
if index <= 0:
self.toolbar.cycle_previous_action.setDisabled(True)
else:
self.toolbar.cycle_previous_action.setDisabled(False)
if index >= self.toolbar.source_select.count() - 1:
self.toolbar.cycle_next_action.setDisabled(True)
else:
self.toolbar.cycle_next_action.setDisabled(False)
def _open_in_specviz(self):
_specviz_instance = self.session.application.new_data_viewer(
SpecVizViewer)
spec1d_data = self._loaded_data['spectrum1d']
spec_data = Spectrum1DRef(
data=spec1d_data.get_component(spec1d_data.id['Flux']).data,
dispersion=spec1d_data.get_component(
spec1d_data.id['Wavelength']).data,
uncertainty=StdDevUncertainty(
spec1d_data.get_component(spec1d_data.id['Uncertainty']).data),
unit="",
name=self.current_row['id'],
wcs=WCS(spec1d_data.header))
_specviz_instance.open_data(spec_data)
def load_selection(self, row):
"""
Processes a row in the MOS catalog by first loading the data set,
updating the stored data components, and then rendering the data on
the visible MOSViz viewer plots.
Parameters
----------
row : :class:`astropy.table.Row`
A row object representing a row in the MOS catalog. Each key
should be a column name.
"""
self.current_row = row
# Get loaders
loader_spectrum1d = SPECTRUM1D_LOADERS[self.catalog.meta["loaders"]
["spectrum1d"]]
loader_spectrum2d = SPECTRUM2D_LOADERS[self.catalog.meta["loaders"]
["spectrum2d"]]
loader_cutout = CUTOUT_LOADERS[self.catalog.meta["loaders"]["cutout"]]
# Get column names
colname_spectrum1d = self.catalog.meta["special_columns"]["spectrum1d"]
colname_spectrum2d = self.catalog.meta["special_columns"]["spectrum2d"]
colname_cutout = self.catalog.meta["special_columns"]["cutout"]
spec1d_data = loader_spectrum1d(row[colname_spectrum1d])
spec2d_data = loader_spectrum2d(row[colname_spectrum2d])
self._update_data_components(spec1d_data, key='spectrum1d')
self._update_data_components(spec2d_data, key='spectrum2d')
basename = os.path.basename(row[colname_cutout])
if basename == "None":
self.render_data(row, spec1d_data, spec2d_data, None)
else:
image_data = loader_cutout(row[colname_cutout])
self._update_data_components(image_data, key='cutout')
self.render_data(row, spec1d_data, spec2d_data, image_data)
def _update_data_components(self, data, key):
"""
Update the data components that act as containers for the displayed
data in the MOSViz viewer. This obviates the need to keep creating new
data components.
Parameters
----------
data : :class:`glue.core.data.Data`
Data object to replace within the component.
key : str
References the particular data set type.
"""
cur_data = self._loaded_data.get(key, None)
if cur_data is None:
self._loaded_data[key] = data
self.session.data_collection.append(data)
else:
cur_data.update_values_from_data(data)
def render_data(self,
row,
spec1d_data=None,
spec2d_data=None,
image_data=None):
"""
Render the updated data sets in the individual plot widgets within the
MOSViz viewer.
"""
self._check_unsaved_comments()
if spec1d_data is not None:
spectrum1d_x = spec1d_data[spec1d_data.id['Wavelength']]
spectrum1d_y = spec1d_data[spec1d_data.id['Flux']]
spectrum1d_yerr = spec1d_data[spec1d_data.id['Uncertainty']]
self.spectrum1d_widget.set_data(x=spectrum1d_x,
y=spectrum1d_y,
yerr=spectrum1d_yerr)
# Try to retrieve the wcs information
try:
flux_unit = spec1d_data.header.get('BUNIT', 'Jy').lower()
flux_unit = flux_unit.replace('counts', 'count')
flux_unit = u.Unit(flux_unit)
except ValueError:
flux_unit = u.Unit("Jy")
try:
disp_unit = spec1d_data.header.get('CUNIT1',
'Angstrom').lower()
disp_unit = u.Unit(disp_unit)
except ValueError:
disp_unit = u.Unit("Angstrom")
self.spectrum1d_widget.axes.set_xlabel(
"Wavelength [{}]".format(disp_unit))
self.spectrum1d_widget.axes.set_ylabel(
"Flux [{}]".format(flux_unit))
if image_data is not None:
wcs = image_data.coords.wcs
self.image_widget.set_image(image_data.get_component(
image_data.id['Flux']).data,
wcs=wcs,
interpolation='none',
origin='lower')
self.image_widget.axes.set_xlabel("Spatial X")
self.image_widget.axes.set_ylabel("Spatial Y")
# Add the slit patch to the plot
ra = row[self.catalog.meta["special_columns"]
["slit_ra"]] * u.degree
dec = row[self.catalog.meta["special_columns"]
["slit_dec"]] * u.degree
slit_width = row[self.catalog.meta["special_columns"]
["slit_width"]]
slit_length = row[self.catalog.meta["special_columns"]
["slit_length"]]
skycoord = SkyCoord(ra, dec, frame='fk5')
xp, yp = skycoord.to_pixel(wcs)
scale = np.sqrt(proj_plane_pixel_area(wcs)) * 3600.
dx = slit_width / scale
dy = slit_length / scale
self.image_widget.draw_rectangle(x=xp, y=yp, width=dx, height=dy)
self.image_widget._redraw()
else:
self.image_widget.setVisible(False)
# Plot the 2D spectrum data last because by then we can make sure that
# we set up the extent of the image appropriately if the cutout and the
# 1D spectrum are present so that the axes can be locked.
if spec2d_data is not None:
wcs = spec2d_data.coords.wcs
xp2d = np.arange(spec2d_data.shape[1])
yp2d = np.repeat(0, spec2d_data.shape[1])
spectrum2d_disp, spectrum2d_offset = spec2d_data.coords.pixel2world(
xp2d, yp2d)
x_min = spectrum2d_disp.min()
x_max = spectrum2d_disp.max()
if image_data is None:
y_min = -0.5
y_max = spec2d_data.shape[0] - 0.5
else:
y_min = yp - dy / 2.
y_max = yp + dy / 2.
extent = [x_min, x_max, y_min, y_max]
self.spectrum2d_widget.set_image(image=spec2d_data.get_component(
spec2d_data.id['Flux']).data,
interpolation='none',
aspect='auto',
extent=extent,
origin='lower')
self.spectrum2d_widget.axes.set_xlabel("Wavelength")
self.spectrum2d_widget.axes.set_ylabel("Spatial Y")
self.spectrum2d_widget._redraw()
# Clear the meta information widget
# NOTE: this process is inefficient
for i in range(self.meta_form_layout.count()):
wid = self.meta_form_layout.itemAt(i).widget()
label = self.meta_form_layout.labelForField(wid)
if label is not None:
label.deleteLater()
wid.deleteLater()
# Repopulate the form layout
# NOTE: this process is inefficient
for col in row.colnames:
if col.lower() not in ["comments", "flag"]:
line_edit = QLineEdit(str(row[col]),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow(col, line_edit)
# Set up comment and flag input/display boxes
if self.comments:
if self.savepath is not None:
if self.savepath == -1:
line_edit = QLineEdit(
os.path.basename("Not Saving to File."),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
else:
line_edit = QLineEdit(os.path.basename(self.savepath),
self.central_widget.meta_form_widget)
line_edit.setReadOnly(True)
self.meta_form_layout.addRow("Save File", line_edit)
self.input_flag = QLineEdit(self.get_flag(),
self.central_widget.meta_form_widget)
self.input_flag.textChanged.connect(self._text_changed)
self.input_flag.setStyleSheet(
"background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Flag", self.input_flag)
self.input_comments = QPlainTextEdit(
self.get_comment(), self.central_widget.meta_form_widget)
self.input_comments.textChanged.connect(self._text_changed)
self.input_comments.setStyleSheet(
"background-color: rgba(255, 255, 255);")
self.meta_form_layout.addRow("Comments", self.input_comments)
self.input_save = QPushButton('Save',
self.central_widget.meta_form_widget)
self.input_save.clicked.connect(self.update_comments)
self.input_save.setDefault(True)
self.input_refresh = QPushButton(
'Reload', self.central_widget.meta_form_widget)
self.input_refresh.clicked.connect(self.refresh_comments)
self.meta_form_layout.addRow(self.input_save, self.input_refresh)
@defer_draw
def set_locked_axes(self, x=None, y=None):
# Here we only change the setting if x or y are not None
# since if set_locked_axes is called with eg. x=True, then
# we shouldn't change the y setting.
if x is not None:
self.spectrum2d_spectrum1d_share.sharex = x
if y is not None:
self.spectrum2d_image_share.sharey = y
self.spectrum1d_widget._redraw()
self.spectrum2d_widget._redraw()
self.image_widget._redraw()
def layer_view(self):
return self._layer_view
def _text_changed(self):
if self.textChangedAt is None:
i = self.toolbar.source_select.currentIndex()
self.textChangedAt = self._index_hash(i)
def _check_unsaved_comments(self):
if self.textChangedAt is None:
return #Nothing to be changed
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
if self.textChangedAt == i:
self.textChangedAt = None
return #This is a refresh
info = "Comments or flags changed but were not saved. Would you like to save them?"
reply = QMessageBox.question(self, '', info,
QMessageBox.Yes | QMessageBox.No)
if reply == QMessageBox.Yes:
self.update_comments(True)
self.textChangedAt = None
def _data_collection_index(self, label):
idx = -1
for i, l in enumerate(self.session.data_collection):
if l.label == label:
idx = i
break
if idx == -1:
return -1
self.data_idx = idx
return idx
def _index_hash(self, i):
"""Local selection index -> Table index"""
if self.mask is not None:
size = self.mask.size
temp = np.arange(size)
return temp[self.mask][i]
else:
return i
def _id_to_index_hash(self, ID, l):
"""Object Name -> Table index"""
for i, name in enumerate(l):
if name == ID:
return i
return None
def get_comment(self):
idx = self.data_idx
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
comp = self.session.data_collection[idx].get_component("comments")
return comp.labels[i]
def get_flag(self):
idx = self.data_idx
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
comp = self.session.data_collection[idx].get_component("flag")
return comp.labels[i]
def send_NumericalDataChangedMessage(self):
idx = self.data_idx
data = self.session.data_collection[idx]
data.hub.broadcast(msg.NumericalDataChangedMessage(data, "comments"))
def refresh_comments(self):
self.input_flag.setText(self.get_flag())
self.input_comments.setPlainText(self.get_comment())
self.input_flag.setStyleSheet("background-color: rgba(255, 255, 255);")
self.textChangedAt = None
def _get_save_path(self):
"""
Try to get save path from other MOSVizViewer instances
"""
for v in self.session.application.viewers[0]:
if isinstance(v, MOSVizViewer):
if v.savepath is not None:
if v.data_idx == self.data_idx:
self.savepath = v.savepath
break
def _setup_save_path(self):
"""
Prompt the user for a file to save comments and flags into.
"""
fail = True
success = False
info = "Where would you like to save comments and flags?"
option = pick_item(
[0, 1], [os.path.basename(self.filepath), "New MOSViz Table file"],
label=info,
title="Comment Setup")
if option == 0:
self.savepath = self.filepath
elif option == 1:
dirname = os.path.dirname(self.filepath)
path = compat.getsavefilename(caption="New MOSViz Table File",
basedir=dirname,
filters="*.txt")[0]
if path == "":
return fail
self.savepath = path
else:
return fail
for v in self.session.application.viewers[0]:
if isinstance(v, MOSVizViewer):
if v.data_idx == self.data_idx:
v.savepath = self.savepath
self._layer_view.refresh()
return success
def update_comments(self, pastSelection=False):
"""
Process comment and flag changes and save to file.
Parameters
----------
pastSelection : bool
True when updating past selections. Used when
user forgets to save.
"""
if self.input_flag.text() == "":
self.input_flag.setStyleSheet("background-color: rgba(255, 0, 0);")
return
i = None
try:
i = int(self.input_flag.text())
except ValueError:
self.input_flag.setStyleSheet("background-color: rgba(255, 0, 0);")
info = QMessageBox.information(self, "Status:",
"Flag must be an int!")
return
self.input_flag.setStyleSheet("background-color: rgba(255, 255, 255);")
idx = self.data_idx
if pastSelection:
i = self.textChangedAt
self.textChangedAt = None
else:
i = self.toolbar.source_select.currentIndex()
i = self._index_hash(i)
data = self.session.data_collection[idx]
comp = data.get_component("comments")
comp.labels.flags.writeable = True
comp.labels[i] = self.input_comments.toPlainText()
comp = data.get_component("flag")
comp.labels.flags.writeable = True
comp.labels[i] = self.input_flag.text()
self.send_NumericalDataChangedMessage()
self.write_comments()
self.textChangedAt = None
def _load_comments(self, label):
"""
Populate the comments and flag columns.
Attempt to load comments from file.
Parameters
----------
label : str
The label of the data in
session.data_collection.
"""
#Make sure its the right data
#(beacuse subset data is masked)
idx = self._data_collection_index(label)
if idx == -1:
return False
data = self.session.data_collection[idx]
#Fill in default comments:
length = data.shape[0]
new_comments = np.array(["" for i in range(length)], dtype=object)
new_flags = np.array(["0" for i in range(length)], dtype=object)
#Fill in any saved comments:
meta = data.meta
obj_names = data.get_component(
self.catalog.meta["special_columns"]["source_id"]).labels
if "MOSViz_comments" in meta.keys():
try:
comments = meta["MOSViz_comments"]
for key in comments.keys():
index = self._id_to_index_hash(key, obj_names)
if index is not None:
line = comments[key]
new_comments[index] = line
except Exception as e:
print("MOSViz Comment Load Failed: ", e)
if "MOSViz_flags" in meta.keys():
try:
flags = meta["MOSViz_flags"]
for key in flags.keys():
index = self._id_to_index_hash(key, obj_names)
if index is not None:
line = flags[key]
new_flags[index] = line
except Exception as e:
print("MOSViz Flag Load Failed: ", e)
#Send to DC
data.add_component(CategoricalComponent(new_flags, "flag"), "flag")
data.add_component(CategoricalComponent(new_comments, "comments"),
"comments")
return True
def write_comments(self):
"""
Setup save file. Write comments and flags to file
"""
if self.savepath is None:
fail = self._setup_save_path()
if fail: return
if self.savepath == -1:
return #Do not save to file option
idx = self.data_idx
data = self.session.data_collection[idx]
save_comments = data.get_component("comments").labels
save_flag = data.get_component("flag").labels
obj_names = data.get_component(
self.catalog.meta["special_columns"]["source_id"]).labels
fn = self.savepath
folder = os.path.dirname(fn)
t = astropy_table.data_to_astropy_table(data)
#Check if load and save dir paths match
temp = os.path.dirname(self.filepath)
if not os.path.samefile(folder, temp):
t['spectrum1d'].flags.writeable = True
t['spectrum2d'].flags.writeable = True
t['cutout'].flags.writeable = True
for i in range(len(t)):
t['spectrum1d'][i] = os.path.abspath(t['spectrum1d'][i])
t['spectrum2d'][i] = os.path.abspath(t['spectrum2d'][i])
t['cutout'][i] = os.path.abspath(t['cutout'][i])
try:
t.remove_column("comments")
t.remove_column("flag")
keys = t.meta.keys()
if "MOSViz_comments" in keys:
t.meta.pop("MOSViz_comments")
if "MOSViz_flags" in keys:
t.meta.pop("MOSViz_flags")
comments = OrderedDict()
flags = OrderedDict()
for i, line in enumerate(save_comments):
if line != "":
line = line.replace("\n", " ")
key = str(obj_names[i])
comments[key] = line
for i, line in enumerate(save_flag):
if line != "0" and line != "":
line = com.replace("\n", " ")
key = str(obj_names[i])
flags[key] = line
if len(comments) > 0:
t.meta["MOSViz_comments"] = comments
if len(flags) > 0:
t.meta["MOSViz_flags"] = flags
t.write(fn, format="ascii.ecsv", overwrite=True)
except Exception as e:
print("Comment write failed:", e)
def closeEvent(self, event):
"""
Clean up the extraneous data components created when opening the
MOSViz viewer by overriding the parent class's close event.
"""
super(MOSVizViewer, self).closeEvent(event)
for data in self._loaded_data.values():
self.session.data_collection.remove(data)
class FileDialog(QDialog):
def __init__(self,
file_name,
job_name,
job_number,
realization,
iteration,
parent=None):
super().__init__(parent)
self.setWindowTitle(
f"{job_name} # {job_number} "
f"Realization: {realization} Iteration: {iteration}")
try:
self._file = open(file_name, "r")
except OSError as error:
self._mb = QMessageBox(
QMessageBox.Critical,
"Error opening file",
error.strerror,
QMessageBox.Ok,
self,
)
self._mb.finished.connect(self.accept)
self._mb.show()
return
self._view = QPlainTextEdit()
self._view.setReadOnly(True)
self._view.setWordWrapMode(QTextOption.NoWrap)
# for moving the actual slider
self._view.verticalScrollBar().sliderMoved.connect(self._update_cursor)
# for mouse wheel and keyboard arrows
self._view.verticalScrollBar().valueChanged.connect(
self._update_cursor)
self._view.setFont(QFontDatabase.systemFont(QFontDatabase.FixedFont))
self._follow_mode = False
self._init_layout()
self._init_thread()
self.show()
@Slot()
def _stop_thread(self):
self._thread.quit()
self._thread.wait()
def _init_layout(self):
self.setMinimumWidth(600)
self.setMinimumHeight(400)
dialog_buttons = QDialogButtonBox(QDialogButtonBox.Ok)
dialog_buttons.accepted.connect(self.accept)
self._copy_all_button = dialog_buttons.addButton(
"Copy All", QDialogButtonBox.ActionRole)
self._copy_all_button.clicked.connect(self._copy_all)
self._follow_button = dialog_buttons.addButton(
"Follow", QDialogButtonBox.ActionRole)
self._follow_button.setCheckable(True)
self._follow_button.toggled.connect(self._enable_follow_mode)
self._enable_follow_mode(self._follow_mode)
layout = QVBoxLayout(self)
layout.addWidget(self._view)
layout.addWidget(dialog_buttons)
def _init_thread(self):
self._thread = QThread()
self._worker = FileUpdateWorker(self._file)
self._worker.moveToThread(self._thread)
self._worker.read.connect(self._append_text)
self._thread.started.connect(self._worker.setup)
self._thread.finished.connect(self._worker.stop)
self._thread.finished.connect(self._worker.deleteLater)
self.finished.connect(self._stop_thread)
self._thread.start()
def _copy_all(self) -> None:
text = self._view.toPlainText()
QApplication.clipboard().setText(text, QClipboard.Clipboard)
pass
def _update_cursor(self, value: int) -> None:
if not self._view.textCursor().hasSelection():
block = self._view.document().findBlockByLineNumber(value)
cursor = QTextCursor(block)
self._view.setTextCursor(cursor)
def _enable_follow_mode(self, enable: bool) -> None:
if enable:
self._view.moveCursor(QTextCursor.End)
self._view.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self._view.verticalScrollBar().setDisabled(True)
self._view.setTextInteractionFlags(Qt.NoTextInteraction)
self._follow_mode = True
else:
self._view.verticalScrollBar().setDisabled(False)
self._view.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
self._view.setTextInteractionFlags(Qt.TextSelectableByMouse
| Qt.TextSelectableByKeyboard)
self._follow_mode = False
def _append_text(self, text: str) -> None:
# Remove trailing newline as appendPlainText adds this
if text[-1:] == "\n":
text = text[:-1]
if self._follow_mode:
self._view.moveCursor(QTextCursor.End)
self._view.appendPlainText(text)
