python-ginga 2.6.1-2 / usr / lib / python2.7 / dist-packages / ginga / rv / plugins / SaveImage.py

#
# SaveImage.py -- Save output images global plugin for Ginga
#
# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
#
"""Save output images global plugin for Ginga."""
from __future__ import absolute_import, division, print_function
from ginga.util.six import itervalues
from ginga.util.six.moves import map

# STDLIB
import os
import shutil

# THIRD-PARTY
from astropy.io import fits

# GINGA
from ginga.GingaPlugin import GlobalPlugin
from ginga.gw import Widgets
from ginga.misc import Bunch
from ginga.util.iohelper import shorten_name

try:
    from ginga.gw.GwHelp import DirectorySelection
except ImportError:  # This is needed for RTD to build
    pass

__all__ = []


class SaveImage(GlobalPlugin):
    """Save images to output files.

    """
    def __init__(self, fv):
        # superclass defines some variables for us, like logger
        super(SaveImage, self).__init__(fv)

        # Image listing
        self.columns = [('Image', 'IMAGE'), ('Mod. Ext.', 'MODEXT')]

        # User preferences. Some are just default values and can also be
        # changed by GUI.
        prefs = self.fv.get_preferences()
        self.settings = prefs.createCategory('plugin_SaveImage')
        self.settings.addDefaults(output_directory = '.',
                                  output_suffix = 'ginga',
                                  include_chname = True,
                                  clobber = False,
                                  modified_only = True,
                                  max_mosaic_size = 1e8,
                                  max_rows_for_col_resize = 5000)
        self.settings.load(onError='silent')

        self.outdir = os.path.abspath(
            self.settings.get('output_directory', '.'))
        self.suffix = self.settings.get('output_suffix', 'ginga')

        self.fv.add_callback('add-image', lambda *args: self.redo())
        self.fv.add_callback('remove-image', lambda *args: self.redo())
        self.fv.add_callback('add-channel',
                             lambda *args: self.update_channels())
        self.fv.add_callback('delete-channel',
                             lambda *args: self.update_channels())

        self.chnames = []
        self.chname = None

        self.gui_up = False

    def build_gui(self, container):
        """Build GUI such that image list area is maximized."""

        vbox, sw, orientation = Widgets.get_oriented_box(container)

        msg_font = self.fv.get_font('sansFont', 12)
        tw = Widgets.TextArea(wrap=True, editable=False)
        tw.set_font(msg_font)
        self.tw = tw

        fr = Widgets.Expander('Instructions')
        fr.set_widget(tw)
        container.add_widget(fr, stretch=0)

        captions = (('Channel:', 'label', 'Channel Name', 'combobox',
                     'Modified only', 'checkbutton'), )
        w, b = Widgets.build_info(captions, orientation=orientation)
        self.w.update(b)

        b.channel_name.set_tooltip('Channel for locating images to save')
        b.channel_name.add_callback('activated', self.select_channel_cb)

        mod_only = self.settings.get('modified_only', True)
        b.modified_only.set_state(mod_only)
        b.modified_only.add_callback('activated', lambda *args: self.redo())
        b.modified_only.set_tooltip("Show only locally modified images")

        container.add_widget(w, stretch=0)

        captions = (('Path:', 'llabel', 'OutDir', 'entry', 'Browse', 'button'),
                    ('Suffix:', 'llabel', 'Suffix', 'entry'))
        w, b = Widgets.build_info(captions, orientation=orientation)
        self.w.update(b)

        b.outdir.set_text(self.outdir)
        b.outdir.set_tooltip('Output directory')
        b.outdir.add_callback('activated', lambda w: self.set_outdir())

        b.browse.set_tooltip('Browse for output directory')
        b.browse.add_callback('activated', lambda w: self.browse_outdir())

        b.suffix.set_text(self.suffix)
        b.suffix.set_tooltip('Suffix to append to filename')
        b.suffix.add_callback('activated', lambda w: self.set_suffix())

        container.add_widget(w, stretch=0)

        self.treeview = Widgets.TreeView(auto_expand=True,
                                         sortable=True,
                                         selection='multiple',
                                         use_alt_row_color=True)
        self.treeview.setup_table(self.columns, 1, 'IMAGE')
        self.treeview.add_callback('selected', self.toggle_save_cb)
        container.add_widget(self.treeview, stretch=1)

        captions = (('Status', 'llabel'), )
        w, b = Widgets.build_info(captions, orientation=orientation)
        self.w.update(b)
        b.status.set_text('')
        b.status.set_tooltip('Status message')
        container.add_widget(w, stretch=0)

        btns = Widgets.HBox()
        btns.set_border_width(4)
        btns.set_spacing(3)

        btn = Widgets.Button('Save')
        btn.set_tooltip('Save selected image(s)')
        btn.add_callback('activated', lambda w: self.save_images())
        btn.set_enabled(False)
        btns.add_widget(btn, stretch=0)
        self.w.save = btn

        btn = Widgets.Button('Close')
        btn.add_callback('activated', lambda w: self.close())
        btns.add_widget(btn, stretch=0)
        btns.add_widget(Widgets.Label(''), stretch=1)
        container.add_widget(btns, stretch=0)

        self.gui_up = True

        # Initialize directory selection dialog
        self.dirsel = DirectorySelection(self.fv.w.root.get_widget())

        # Generate initial listing
        self.update_channels()

    def instructions(self):
        self.tw.set_text("""Enter output directory and suffix, if different than default. Left click to select image name to save. Multiple images can be selected using click with Shift or CTRL key. Click Save to save the selected image(s).

Output image will have the filename of <inputname>_<suffix>.fits.""")

    def redo(self, *args):
        """Generate listing of images that user can save."""
        if not self.gui_up:
            return

        mod_only = self.w.modified_only.get_state()
        treedict = Bunch.caselessDict()
        self.treeview.clear()
        self.w.status.set_text('')

        channel = self.fv.get_channel(self.chname)
        if channel is None:
            return

        # Only list modified images for saving. Scanning Datasrc is enough.
        if mod_only:
            all_keys = channel.datasrc.keys(sort='alpha')

        # List all images in the channel.
        else:
            all_keys = channel.get_image_names()

        # Extract info for listing and saving
        for key in all_keys:
            iminfo = channel.get_image_info(key)
            path = iminfo.get('path')
            idx = iminfo.get('idx')
            t = iminfo.get('time_modified')

            if path is None:  # Special handling for generated buffer, eg mosaic
                infile = key
                is_fits = True
            else:
                infile = os.path.basename(path)
                infile_ext = os.path.splitext(path)[1]
                infile_ext = infile_ext.lower()
                is_fits = False

                if 'fit' in infile_ext:
                    is_fits = True

            # Only list FITS files unless it is Ginga generated buffer
            if not is_fits:
                continue

            # Only list modified buffers
            if mod_only and t is None:
                continue

            # More than one ext modified, append to existing entry
            if infile in treedict:
                if t is not None:
                    treedict[infile].extlist.add(idx)
                    elist = sorted(treedict[infile].extlist)
                    treedict[infile].MODEXT = ';'.join(
                        map(self._format_extname, elist))

            # Add new entry
            else:
                if t is None:
                    s = ''
                    extlist = set()
                else:
                    s = self._format_extname(idx)
                    extlist = set([idx])
                treedict[infile] = Bunch.Bunch(
                    IMAGE=infile, MODEXT=s, extlist=extlist, path=path)

        self.treeview.set_tree(treedict)

        # Resize column widths
        n_rows = len(treedict)
        if n_rows == 0:
            self.w.status.set_text('Nothing available for saving')
        elif n_rows < self.settings.get('max_rows_for_col_resize', 5000):
            self.treeview.set_optimal_column_widths()
            self.logger.debug('Resized columns for {0} row(s)'.format(n_rows))

    def update_channels(self):
        """Update the GUI to reflect channels and image listing.
        """
        if not self.gui_up:
            return

        self.logger.debug("channel configuration has changed--updating gui")
        try:
            channel = self.fv.get_channel(self.chname)

        except KeyError:
            channel = self.fv.get_channel_info()

        if channel is None:
            raise ValueError('No channel available')

        self.chname = channel.name

        w = self.w.channel_name
        w.clear()

        self.chnames = list(self.fv.get_channel_names())
        #self.chnames.sort()
        for chname in self.chnames:
            w.append_text(chname)

        # select the channel that is the current one
        try:
            i = self.chnames.index(channel.name)
        except IndexError:
            i = 0
        self.w.channel_name.set_index(i)

        # update the image listing
        self.redo()

    def select_channel_cb(self, w, idx):
        self.chname = self.chnames[idx]
        self.logger.debug("channel name changed to '%s'" % (self.chname))
        self.redo()

    def _format_extname(self, ext):
        """Pretty print given extension name and number tuple."""
        if ext is None:
            outs = ext
        else:
            outs = '{0},{1}'.format(ext[0], ext[1])
        return outs

    def browse_outdir(self):
        """Browse for output directory."""
        self.dirsel.popup(
            'Select directory', self.w.outdir.set_text, initialdir=self.outdir)
        self.set_outdir()

    def set_outdir(self):
        """Set output directory."""
        dirname = self.w.outdir.get_text()
        if os.path.isdir(dirname):
            self.outdir = dirname
            self.logger.debug('Output directory set to {0}'.format(self.outdir))
        else:
            self.w.outdir.set_text(self.outdir)
            self.logger.error('{0} is not a directory'.format(dirname))

    def set_suffix(self):
        """Set output suffix."""
        self.suffix = self.w.suffix.get_text()
        self.logger.debug('Output suffix set to {0}'.format(self.suffix))

    def _write_history(self, pfx, hdu, linechar=60, indentchar=2):
        """Write change history to given HDU header.
        Limit each HISTORY line to given number of characters.
        Subsequent lines of the same history will be indented.
        """
        channel = self.fv.get_channel(self.chname)
        if channel is None:
            return

        history_plgname = 'ChangeHistory'
        try:
            history_obj = self.fv.gpmon.getPlugin(history_plgname)
        except:
            self.logger.error(
                '{0} plugin is not loaded. No HISTORY will be written to '
                '{1}.'.format(history_plgname, pfx))
            return

        if channel.name not in history_obj.name_dict:
            self.logger.error(
                '{0} channel not found in {1}. No HISTORY will be written to '
                '{2}.'.format(channel.name, history_plgname, pfx))
            return

        file_dict = history_obj.name_dict[channel.name]
        chistory = []
        ind = ' ' * indentchar

        # NOTE: List comprehension too slow!
        for key in file_dict:
            if not key.startswith(pfx):
                continue
            for bnch in itervalues(file_dict[key]):
                chistory.append('{0} {1}'.format(bnch.MODIFIED, bnch.DESCRIP))

        # Add each HISTORY prettily into header, sorted by timestamp
        for s in sorted(chistory):
            for i in range(0, len(s), linechar):
                subs = s[i:i+linechar]
                if i > 0:
                    subs = ind + subs.lstrip()
                hdu.header.add_history(subs)

    def _write_header(self, image, hdu):
        """Write header from image object to given HDU."""
        hduhdr = hdu.header

        # Ginga image header object for the given extension only.
        # Cannot use get_header() because that might also return PRI hdr.
        ghdr = image.metadata['header']

        for key in ghdr:
            # Need this to avoid duplication because COMMENT is a weird field
            if key.upper() == 'COMMENT':
                continue

            bnch = ghdr.get_card(key)

            # Insert new keyword
            if key not in hduhdr:
                hduhdr[key] = (bnch.value, bnch.comment)

            # Update existing keyword
            elif hduhdr[key] != bnch.value:
                hduhdr[key] = bnch.value

    def _write_mosaic(self, key, outfile):
        """Write out mosaic data (or any new data generated within Ginga)
        to single-extension FITS.

        """
        maxsize = self.settings.get('max_mosaic_size', 1e8)  # Default 10k x 10k
        channel = self.fv.get_channel(self.chname)
        image = channel.datasrc[key]

        # Prevent writing very large mosaic
        if (image.width * image.height) > maxsize:
            s = 'Mosaic too large to be written {0}'.format(image.shape)
            self.w.status.set_text(s)
            self.logger.error(s)
            return

        # Insert mosaic data and header into output HDU
        hdu = fits.PrimaryHDU(image.get_data())
        self._write_header(image, hdu)

        # Write history to PRIMARY
        self._write_history(key, hdu)

        # Write to file
        hdu.writeto(outfile, clobber=True)

    def _write_mef(self, key, extlist, outfile):
        """Write out regular multi-extension FITS data."""
        channel = self.fv.get_channel(self.chname)
        with fits.open(outfile, mode='update') as pf:
            # Process each modified data extension
            for idx in extlist:
                k = '{0}[{1}]'.format(key, self._format_extname(idx))
                image = channel.datasrc[k]

                # Insert data and header into output HDU
                pf[idx].data = image.get_data()
                self._write_header(image, pf[idx])

            # Write history to PRIMARY
            self._write_history(key, pf['PRIMARY'])

    def toggle_save_cb(self, w, res_dict):
        """Only enable saving if something is selected."""
        if len(res_dict) > 0:
            self.w.save.set_enabled(True)
        else:
            self.w.save.set_enabled(False)

    def save_images(self):
        """Save selected images.

        This uses Astropy FITS package to save the outputs no matter
        what user chose to load the images.

        """
        res_dict = self.treeview.get_selected()
        clobber = self.settings.get('clobber', False)
        self.treeview.clear_selection()  # Automatically disables Save button

        # If user gives empty string, no suffix.
        if self.suffix:
            sfx = '_' + self.suffix
        else:
            sfx = ''

        # Also include channel name in suffix. This is useful if user likes to
        # open the same image in multiple channels.
        if self.settings.get('include_chname', True):
            sfx += '_' + self.chname

        # Process each selected file. Each can have multiple edited extensions.
        for infile in res_dict:
            f_pfx = os.path.splitext(infile)[0]  # prefix
            f_ext = '.fits'  # Only FITS supported
            oname = f_pfx + sfx + f_ext
            outfile = os.path.join(self.outdir, oname)

            self.w.status.set_text(
                'Writing out {0} to {1} ...'.format(shorten_name(infile, 10),
                                                    shorten_name(oname, 10)))
            self.logger.debug(
                'Writing out {0} to {1} ...'.format(infile, oname))

            if os.path.exists(outfile) and not clobber:
                self.logger.error('{0} already exists'.format(outfile))
                continue

            bnch = res_dict[infile]

            if bnch.path is None or not os.path.isfile(bnch.path):
                self._write_mosaic(f_pfx, outfile)
            else:
                shutil.copyfile(bnch.path, outfile)
                self._write_mef(f_pfx, bnch.extlist, outfile)

            self.logger.info('{0} written'.format(outfile))

        self.w.status.set_text('Saving done, see log')

    def close(self):
        self.fv.stop_global_plugin(str(self))

    def start(self):
        self.instructions()
        self.resume()

    def resume(self):
        # turn off any mode user may be in
        try:
            self.modes_off()
        except AttributeError:
            pass

        self.fv.show_status('See instructions')

    def stop(self):
        self.gui_up = False
        self.fv.show_status('')

    def __str__(self):
        """
        This method should be provided and should return the lower case
        name of the plugin.
        """
        return 'saveimage'


# Replace module docstring with config doc for auto insert by Sphinx.
# In the future, if we need the real docstring, we can append instead of
# overwrite.
from ginga.util.toolbox import generate_cfg_example
__doc__ = generate_cfg_example('plugin_SaveImage', package='ginga')