import os
from collections import OrderedDict

import numpy as np
from pathlib import Path
from qtpy import compat
from qtpy.QtCore import Signal
from qtpy.QtWidgets import QWidget, QLineEdit, QMessageBox, QPlainTextEdit, QPushButton
from qtpy.uic import loadUi

from glue.core import message as msg
from glue.core import Subset
from glue.core.exceptions import IncompatibleAttribute
from glue.core.data_exporters import astropy_table
from glue.core.component import CategoricalComponent
from glue.viewers.common.qt.data_viewer import DataViewer
from glue.utils.matplotlib import defer_draw
from glue.utils.decorators import avoid_circular
from glue.utils.qt import pick_item, get_qapp

from astropy.table import Table
from astropy.nddata.nduncertainty import StdDevUncertainty
from astropy import units as u
from astropy.wcs import WCS
from astropy.coordinates import SkyCoord
from astropy.wcs.utils import proj_plane_pixel_area

try:
    from specviz.third_party.glue.viewer import SpecvizDataViewer
except ImportError:
    SpecvizDataViewer = None

from ..widgets.toolbars import MOSViewerToolbar
from ..widgets.plots import Line1DWidget, Spectrum2DWidget, DrawableImageWidget
from ..loaders.loader_selection import confirm_loaders_and_column_names
from ..loaders.utils import SPECTRUM1D_LOADERS, SPECTRUM2D_LOADERS, CUTOUT_LOADERS, LEVEL2_LOADERS
from ..widgets.viewer_options import OptionsWidget
from ..widgets.share_axis import SharedAxisHelper
from .. import UI_DIR
from ..widgets.layer_widget import SimpleLayerWidget
from ..controls.slits.slit_controller import SlitController

from specviz.widgets.workspace import Workspace
from specviz.third_party.glue.utils import glue_data_to_spectrum1d

__all__ = ['MOSVizViewer']


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)

import os
from collections import OrderedDict

import numpy as np
from pathlib import Path
from qtpy import compat
from qtpy.QtCore import Signal
from qtpy.QtWidgets import QWidget, QLineEdit, QMessageBox, QPlainTextEdit, QPushButton
from qtpy.uic import loadUi

from glue.core import message as msg
from glue.core import Subset
from glue.core.exceptions import IncompatibleAttribute
from glue.core.data_exporters import astropy_table
from glue.core.component import CategoricalComponent
from glue.viewers.common.qt.data_viewer import DataViewer
from glue.utils.matplotlib import defer_draw
from glue.utils.decorators import avoid_circular
from glue.utils.qt import pick_item, get_qapp

from astropy.table import Table
from astropy.nddata.nduncertainty import StdDevUncertainty
from astropy import units as u
from astropy.wcs import WCS
from astropy.coordinates import SkyCoord
from astropy.wcs.utils import proj_plane_pixel_area

try:
    from specviz.third_party.glue.viewer import SpecvizDataViewer
except ImportError:
    SpecvizDataViewer = None

from ..widgets.toolbars import MOSViewerToolbar
from ..widgets.plots import Line1DWidget, Spectrum2DWidget, DrawableImageWidget
from ..loaders.loader_selection import confirm_loaders_and_column_names
from ..loaders.utils import SPECTRUM1D_LOADERS, SPECTRUM2D_LOADERS, CUTOUT_LOADERS, LEVEL2_LOADERS
from ..widgets.viewer_options import OptionsWidget
from ..widgets.share_axis import SharedAxisHelper
from .. import UI_DIR
from ..widgets.layer_widget import SimpleLayerWidget
from ..controls.slits.slit_controller import SlitController

from specviz.widgets.workspace import Workspace
from specviz.third_party.glue.utils import glue_data_to_spectrum1d

__all__ = ['MOSVizViewer']


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)

# Define some data containers Setup the MOSView viewer interface. # 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 # 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. # Set the splitter stretch factors # Keep the left and right splitters in sync otherwise the axes don't line up # Set the central widget # Define the options widget # Trigger a sync between the splitters Connects gui elements to event calls. # Connect the selection event for the combo box to what's displayed # Connect the exposure selection event # Connect the specviz button # Connect slit previous and next buttons # Connect exposure previous and next buttons # Connect the toolbar axes setting actions Initialize the custom toolbar for the MOSViz viewer. 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. # We can relax the following requirement if we make the slit parameters # optional # Make sure the loaders and column names are correct 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. # We can relax the following requirement if we make the slit parameters # optional # Block of code to bypass the loader_selection gui ######################################################### # Deimos data ######################################################### Processes subset messages from the central communication hub.          Parameters         ----------         subset :             Subset object. Update data message.          Parameters         ----------         message : :class:`glue.core.message.Message`             Data message object. Add subset message.          Parameters         ----------         message : :class:`glue.core.message.Message`             Subset message object. Update subset message.          Parameters         ----------         message : :class:`glue.core.message.Message`             Update message object. Remove subset message.          Parameters         ----------         message : :class:`glue.core.message.Message`             Subset message object. 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. # Clear the table #Returns bool # Update gui elements Updates the :class:`qtpy.QtWidgets.QComboBox` widget with the         appropriate source `id`s from the MOS catalog. # For level 3-only data. # 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. # 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. # Clear the reference to ensure no qt dangling pointers # Create a new Spectrum1D object from the flux data attribute of # the incoming data # Create a DataItem from the Spectrum1D object, which adds the data # to the internel specviz model 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. # Get loaders # Get column names Loads the level 2 exposure into the 2D spectrum plot widget.          It can also load back the level 3 spectrum. 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. Render the updated data sets in the individual plot widgets within the         MOSViz viewer. # TODO: This should not be needed. Must explore why the core model # is out of sync with the proxy model. # Clear the specviz model of any rendered plot items # Create a new Spectrum1D object from the flux data attribute of # the incoming data # Create a DataItem from the Spectrum1D object, which adds the data # to the internel specviz model # Get the PlotDataItem rendered via the plot's proxy model and # ensure that it is visible in the plot # Explicitly let the plot widget know that data items have changed # Add the slit patch to the plot # 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. # Clear the meta information widget # NOTE: this process is inefficient # Repopulate the form layout # NOTE: this process is inefficient # Set up comment and flag input/display boxes # By default, displays the level 3 spectrum. The level 2 # data is plotted elsewhere, driven by the exposure_select # combo box signals. # 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. # Populates the level 2 exposures combo box # 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. # Lock the x axis if x is True # Call the slot to update the axis linking initially # FIXME: Currently, this does not work for some reason. # Unlock the x axis if x is False #Nothing to be changed #This is a refresh Local selection index -> Table index Object Name -> Table index # TODO: Update once units infrastructure is in place Try to get save path from other MOSVizViewer instances Prompt the user for a file to save comments and flags into. Process comment and flag changes and save to file.          Parameters         ----------         pastSelection : bool             True when updating past selections. Used when             user forgets to save. 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) #Fill in default comments: #Fill in any saved comments: #Send to DC Setup save file. Write comments and flags to file #Do not save to file option #Check if load and save dir paths match Clean up the extraneous data components created when opening the         MOSViz viewer by overriding the parent class's close event.