Merge pull request #63 from sosey/notebook

funcational updates for examine class

docs/rtd-pip-requirements

@@ -4,4 +4,4 @@ numpy
 matplotlib
 Cython
 ginga
-jupyter
+ipython

imexam/connect.py

@@ -107,6 +107,8 @@ def setlog(self, filename=None, on=True, level=logging.DEBUG):
 
     def close(self):
         """Close the window and end connection."""
+        # make sure all the plots are closed
+        self.exam._close_plots()
         self.window.close()
 
     def imexam(self):
@@ -137,7 +139,7 @@ def reopen(self):
 
     def grab(self):
         """Display a snapshop of the current image in the browser window."""
-        self.window.grab()
+        return self.window.grab()
 
     def get_data_filename(self):
         """Return the filename for the data in the current window."""
@@ -316,12 +318,12 @@ def get_image(self):
         """Return the full image object, not just the numpy array."""
         return self.window.get_image()
 
-    def get_header(self):
+    def get_header(self, **kwargs):
         """Return the current fits header as a string.
 
         None is returned if there's a problem
         """
-        return self.window.get_header()
+        return self.window.get_header(**kwargs)
 
     def grid(self, *args, **kwargs):
         """Convenience method to turn the grid on and off.

imexam/ds9_viewer.py

@@ -1048,10 +1048,11 @@ def get_image(self):
                for the full object")
         self.get_data()
 
-    def get_header(self):
+    def get_header(self, fitsobj=False):
         """Return the current fits header.
 
         The return value is the string or None if there's a problem
+        If fits is True  then a fits header object is returned instead
         """
         # TODO return the simple header for arrays which are loaded
 
@@ -1060,11 +1061,14 @@ def get_header(self):
             self._set_frameinfo()
 
         if self._viewer[frame]['filename']:
-            try:
-                header = self.get("fits header")
-            except XpaException as e:
-                print("XPA Exception getting header: {0}".format(e))
-                return None
+            if fitsobj:
+                header = fits.getheader(self._viewer[frame]['filename'])
+            else:
+                try:
+                    header = self.get("fits header")
+                except XpaException as e:
+                    print("XPA Exception getting header: {0}".format(e))
+                    return None
 
             return header
         else:
@@ -1098,7 +1102,7 @@ def embed(self):
         """Embed the viewer in a notebook."""
         print("Not Implemented for DS9")
 
-    def load_fits(self, fname="", extver=1, extname=None):
+    def load_fits(self, fname="", extver=None, extname=None, mecube=False):
         """convenience function to load fits image to current frame.
 
         Parameters
@@ -1113,6 +1117,9 @@ def load_fits(self, fname="", extver=1, extname=None):
 
         extname: string, optional
             The name (EXTNAME in the header) of the image to load
+        
+        mecube: bool, optional
+            If mecube is True, load the fits file as a cube into ds9
 
         Notes
         -----
@@ -1132,14 +1139,20 @@ def load_fits(self, fname="", extver=1, extname=None):
         frame = self.frame()
         if not frame:
             frame = 1  # load into first frame
+        if not extver:
+            extver = 1
 
         if fname:
             # see if the image is MEF or Simple
             fname = os.path.abspath(fname)
 
             # strip the extensions for now
             shortname = fname.split("[")[0]
-            cstring = util.verify_filename(shortname, extver, extname)
+            if mecube:
+                cstring = "mecube {0:s}".format(shortname)
+            else:
+                cstring = util.verify_filename(shortname, extver, extname)
+                print(cstring)
             self.set(cstring)
             self._set_frameinfo()
             # make sure any previous reference is reset
@@ -1655,13 +1668,13 @@ def grab(self):
         """Make a copy of the image view."""
         backend = get_backend().lower()
         supported = ["nbagg", "tkagg", "qt4agg"]
-        if backend in supported or "pylab" in backend:
-                fname = self.snapsave(format="png")
+        fname = self.snapsave(format="png")
+        if "nbagg" in backend:  # save inside the notebook
                 data = mpimage.imread(fname)
                 plt.clf()
-                plt.imshow(data, origin="upper")
+                return plt.imshow(data, origin="upper")
         else:
-            print("Not supported for {0:s}".format(backend))
+            print("Notebook embedding not supported for {0:s}".format(backend))
 
     def view(self, img):
         """Display numpy image array to current frame.
@@ -1703,7 +1716,7 @@ def view(self, img):
                 raise UnsupportedDatatypeException(e)
 
             option = "[xdim={0:d},ydim={1:d},bitpix={2:d}{3:s}]".format(xdim,
-                        ydim,bitpix, endianness)
+                            ydim, bitpix, endianness)
             try:
                 self.set("array " + option, arr_str)
                 self._set_frameinfo()
@@ -1753,5 +1766,6 @@ def reopen(self):
         print("Not available for DS9, start a new object instead")
         raise NotImplementedError
 
+
 atexit.register(ds9._purge_tmp_dirs)
 atexit.register(ds9._stop_running_process)

imexam/ginga_viewer.py

@@ -1,4 +1,4 @@
-"""Licensed under a 3-clause BSD style license - see LICENSE.rst.
+"""Licensed under a 3-clause BSD style license - see LICENSE.rst
 
    This class supports communication with a Ginga-based viewer.
    For default key and mouse shortcuts in a Ginga window, see:
@@ -12,7 +12,6 @@
 import warnings
 import threading
 import numpy as np
-from matplotlib import get_backend
 
 from . import util
 from astropy.io import fits
@@ -24,8 +23,8 @@
 from ginga.util import paths
 from ginga.util import wcsmod
 
-wcsmod.use('AstropyWCS')
 
+wcsmod.use('AstropyWCS')
 
 # module variables
 _matplotlib_cmaps_added = False
@@ -39,23 +38,23 @@
 class ginga_general(object):
 
     """ A base class which controls all interactions between the user and the
-    ginga widget
+    ginga widget.
 
-        The ginga contructor creates a new window using the
-        ginga backend.
+    The ginga contructor creates a new window using the
+    ginga backend.
 
-        Parameters
-        ----------
-        close_on_del : boolean, optional
-            If True, try to close the window when this instance is deleted.
+    Parameters
+    ----------
+    close_on_del : boolean, optional
+        If True, try to close the window when this instance is deleted.
 
 
-        Attributes
-        ----------
-        view: Ginga view object
-             The object instantiated from a Ginga view class
+    Attributes
+    ----------
+    view: Ginga view object
+         The object instantiated from a Ginga view class
 
-        exam: imexamine object
+    exam: imexamine object
     """
 
     def __init__(self, exam=None, close_on_del=True, logger=None, port=None):
@@ -65,15 +64,13 @@ def __init__(self, exam=None, close_on_del=True, logger=None, port=None):
         -----
         Ginga viewers all need a logger, if none is provided it will create one
 
-        the port option is for use in the Jupyter notebook since the server
+        The port option is for use in the Jupyter notebook since the server
         displays the image to a distict port. The user can choose to have
         multiple windows open at the same time as long as they have different
-        ports.
+        ports. If no port is specified, this class will choose an open port.
 
         """
         global _matplotlib_cmaps_added
-        if port is None:
-            port = 667
         self._port = port
         self.exam = exam
         self._close_on_del = close_on_del
@@ -435,7 +432,7 @@ def disp_header(self):
         self.get_header()
 
     def get_header(self):
-        """Return current fits header as string or None if there's a problem."""
+        """Return current fits header as string, None if there's a problem."""
 
         # TODO return the simple header for arrays which are loaded
 
@@ -486,6 +483,7 @@ def _key_press_imexam(self, canvas, keyname):
         if keyname == 'q':
             # temporarily switch to non-imexam mode
             self._release()
+            self.exam._close_plots()
             return True
 
         if keyname == 'backslash':
@@ -846,7 +844,7 @@ def show_window_commands(self):
 
     def grab(self):
         # if self.ginga_view:
-        self.ginga_view.show()
+        return self.ginga_view.show()
 
 
 class ginga(ginga_general):
@@ -872,8 +870,6 @@ def __init__(self, exam=None, close_on_del=True, logger=None, port=None,
         self.use_opencv = use_opencv
         self._host = host
         self._server = None
-        if port is None:
-            port = 9904
         self._port = port
 
         super(ginga, self).__init__(exam=exam, close_on_del=close_on_del,
@@ -890,11 +886,12 @@ def _open_browser(self):
                 doc directory for the HTML help pages")
             print("Open a new browser window for: {}".format(self.ginga_view.url()))
 
-    def _create_viewer(self, bind_prefs, viewer_prefs, opencv=False, threads=1):
+    def _create_viewer(self, bind_prefs, viewer_prefs,
+                       opencv=False, threads=1):
         """Ginga setup for data display in an HTML5 browser."""
         from ginga.web.pgw import Widgets
 
-        # Set this to True if you have a non-buggy python OpenCv bindings
+        # Set opencv to True if you have a non-buggy python OpenCv bindings
         # --it greatly speeds up some operations
         self.use_opencv = opencv
         self._threads = threads
@@ -926,29 +923,33 @@ def _start_server(self):
         from ginga.web.pgw import ipg
         if not self._port:
             import socket
+            import errno
             socket.setdefaulttimeout(0.05)
-            ports = [p for p in range(5800, 6000) if socket.socket().connect_ex(('127.0.0.1', p)) != 10035]
-            self._port = ports.pop()
+            ports = [p for p in range(8800, 9000) if
+                     socket.socket().connect_ex(('127.0.0.1', p)) not in
+                     (errno.EAGAIN, errno.EWOULDBLOCK)]
+            self._port = ports[-1]
 
         self._server = ipg.make_server(host=self._host,
                                        port=self._port,
                                        use_opencv=self.use_opencv,
                                        numthreads=self._threads)
 
-        backend = get_backend().lower()
-        no_ioloop = False  # works best with qtconsole
-        if 'nbagg' in backend:
-            no_ioloop = True  # assume in notebook
-        elif "pylab" in backend:
-            raise NotImplementedError
-        elif "qt4agg" in backend:
-            raise NotImplementedError
-        elif "tkagg" in backend:
-            print("If you aren't in the notebook and have problems with\
-                   graphics, try switching to jupyter console")
+        try:
+            backend_check = get_ipython().config
+        except NameError:
+            backend_check = []
+        no_ioloop = False  # ipython terminal
+        if 'IPKernelApp' in backend_check:
+            no_ioloop = True  # jupyter console and notebook
 
         self._server.start(no_ioloop=no_ioloop)
 
+    def _shutdown(self):
+        self._server.stop()  # stop accepting connections
+        print('Stopped http server')
+
+
     def close(self):
-        """Close the viewing window"""
-        print("You must close the image window by hand")
+        """Close the viewing window."""
+        self._shutdown()