Merge pull request #156 from sosey/release-prep

Prepping to release 0.8.1
spacetelescope · Dec 14, 2018 · b66a483 · b66a483
2 parents 4526223 + f587d30
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,5 +1,7 @@
 version 0.8.1dev (unreleased)
 -----------------------------
+** THIS WILL BE THE LAST VERSION THAT SUPPORT Python 2.7 **
+
 - travis and appveyor testing updates
 - radial profile plot centering fixed to more correctly calculate the fractional center offsets
 - cumulative radial profile flux calculation should now be correct
@@ -15,6 +17,7 @@ version 0.8.1dev (unreleased)
 - new options added to the aperture phot parameter set that allow users to plot the used apertures
 - ZScaleInterval added from astropy.virtualization to set the color range on the data for aperture photometry plot
 - replaced the sigma to fwhm lambda with the astropy constant for conversion
+- added cursor move recognition using the arrow keys during the imexam loop, however, depending how the user has their windowing focus set, the DS9 window may loose focus, forcing them to move the cursor manually back to the window. Cursor moves are only implemented for DS9, not Ginga.
 
 version 0.8.0 (released)
 ------------------------

diff --git a/README.rst b/README.rst
@@ -78,25 +78,59 @@ Try turning off the resume state:
     defaults write org.python.python ApplePersistenceIgnoreState NO
 
 
-If you are having display issues, some build problems may exist with the dependency packages which deal with backend graphics, try setting your matplotlib backend to Qt4Agg. You can set this in your .matplotlib/matplotlibrc file. You may also want to switch your matplotlib backend to Qt if you have a mac with the default MacOS backend specified. If you don't already have matplotlibrc file in your home directory, you can download one from their documentation: http://matplotlib.org/_static/matplotlibrc
+
+Contributing
+============
+Please open a new issue or new pull request for bugs, feedback, or new features
+you would like to see.   If there is an issue you would like to work on, please
+leave a comment and we will be happy to assist.   New contributions and
+contributors are very welcome!
+
+New to github or open source projects?  If you are unsure about where to start
+or haven't used github before, please feel free to contact `@sosey`.
+Want more information about how to make a contribution?  Take a look at
+the astropy `contributing`_ and `developer`_ documentation.
+
+Feedback and feature requests?   Is there something missing you would like
+to see?  Please open an issue or send an email to  `@sosey`. imexam follows the `Astropy Code of Conduct`_ and strives to provide a
+welcoming community to all of our users and contributors.
+
+
+License
+=======
+imexam is licensed under a 3-clause BSD style license (see the
+``licenses/LICENSE.rst`` file).
+
+.. _AstroPy: http://www.astropy.org/
+.. _contributing: http://docs.astropy.org/en/stable/index.html#contributing
+.. _developer: http://docs.astropy.org/en/stable/index.html#developer-documentation
+.. _Astropy Code of Conduct:  http://www.astropy.org/about.html#codeofconduct
+
+
+
+Quick Instructions
+==================
+If you are having display issues, and you are using TkAgg, try setting your matplotlib backend to Qt4Agg or Qt5Agg. You can set this in your .matplotlib/matplotlibrc file. You may also want to switch your matplotlib backend to Qt if you have a mac with the default MacOS backend specified. If you don't already have matplotlibrc file in your home directory, you can download one from their documentation: http://matplotlib.org/_static/matplotlibrc
+
 
 ::
 
-inside ~/.matplotlib/matplotlibrc:
+    inside ~/.matplotlib/matplotlibrc:
     backend: Qt4Agg
 
 
-
 Using the Ginga HTML5 Viewer
 ----------------------------
 
-If you have installed Ginga, you can use the HTML5 viewer for image display with either a python terminal, jupyter console, qtconsole or Jypyter notebook session. If you are using a Windows machine you should install ginga to use as the viewer with this package. Make sure that you have installed the latest version, or you can download the development code here: https://github.com/ejeschke/ginga.  There's also a new ginga plugin for imexam which is in the ginga repository in the experimental directory. This will load the imexam plotting and analysis library into the ginga gui framework.
+If you have installed Ginga, you can use the HTML5 viewer for image display with either a jupyter console, qtconsole or Jupyter notebook session. If you are using a Windows machine you should install ginga to use as the viewer with this package. Make sure that you have installed the latest version, or you can download the development code here: https://github.com/ejeschke/ginga.  
+
+There is also a ginga plugin for imexam which is in the ginga repository in the experimental directory. This will load the imexam plotting and analysis library into the ginga gui framework.
 
 Starting a connection to a Ginga HTML5 canvas backend for browser and Jupyter viewing:
 
 ::
 
-    a=imexam.connect(viewer='ginga')
+    a = imexam.connect(viewer='ginga')
 
 You can optionally provide a port number to which the viewer is connected as well:
 
@@ -105,10 +139,39 @@ You can optionally provide a port number to which the viewer is connected as wel
     a=imexam.connect(viewer='ginga', port=9856)
 
 
+Using imexam with DS9
+---------------------
+From a python terminal: using either the TkAGG or QT4Agg/QT5Agg backends:
+
+
+::
+
+    import imexam
+    a = imexam.connect()
+    a.imexam()
+
+From an ipython terminal: using either the TkAgg or QT4Agg/QT5Agg backends. 
+
+::
+
+    import imexam
+    a = imexam.connect()
+
+If you are using TkAGG as the backend, from an ipython terminal, you may need to ctrl-D, then select n, to closeout the plotting window. This should not happen if you are running TkAgg and running from a regular python terminal. Looking into the closeout issue with TkAgg now.
+
+From jupyter console/qtconsole: startup with the matplotlib magics to use the backend you specified for display:
+
+::
+
+    In [1]: %matplotlib
+    import imexam
+    a = imexam.connect()                                                                                                                                                                                 
+
+If you are using the Qt4Agg/Qt5Agg backend with ginga, the plots will display in the console window
+
 
 Launching multiple DS9 windows
 ------------------------------
-
 You can launch multiple ds9 windows either from this package or the command line. DS9 can be used to view images and arrays from any of the python terminals, consoles or the Jupyter notebook.
 
 If you launch ds9 from outside the imexam package, you need supply the name of the window to imexam, this can be done in one of 2 ways:
@@ -156,7 +219,10 @@ Connecting to a DS9 window which was started from the system prompt:
 Examples can be found in the package documentation, online documentation, and imexam.display_help() will pull up the installed package documentation in a web browser. You can also download the examply Jupyter notebooks available in the example_notebooks directory above.
 
 
-You can also just load the plotting library and NOT connect to any viewer:
+You can also just load the plotting library for use without a viewer:
+---------------------------------------------------------------------
+This is useful when you want to make batch plots or return information from scripts.
+You can also save the lotting data returned and use it futher, or design your own plot.
 
 ::
 
@@ -172,32 +238,3 @@ You can also just load the plotting library and NOT connect to any viewer:
 
     plots.set_data(data)
     plots.plot_line(35,45)
-
-Contributing
-------------
-
-Please open a new issue or new pull request for bugs, feedback, or new features
-you would like to see.   If there is an issue you would like to work on, please
-leave a comment and we will be happy to assist.   New contributions and
-contributors are very welcome!
-
-New to github or open source projects?  If you are unsure about where to start
-or haven't used github before, please feel free to contact `@sosey`.
-Want more information about how to make a contribution?  Take a look at
-the astropy `contributing`_ and `developer`_ documentation.
-
-Feedback and feature requests?   Is there something missing you would like
-to see?  Please open an issue or send an email to  `@sosey`. imexam follows the `Astropy Code of Conduct`_ and strives to provide a
-welcoming community to all of our users and contributors.
-
-
-License
--------
-
-imexam is licensed under a 3-clause BSD style license (see the
-``licenses/LICENSE.rst`` file).
-
-.. _AstroPy: http://www.astropy.org/
-.. _contributing: http://docs.astropy.org/en/stable/index.html#contributing
-.. _developer: http://docs.astropy.org/en/stable/index.html#developer-documentation
-.. _Astropy Code of Conduct:  http://www.astropy.org/about.html#codeofconduct
diff --git a/docs/imexam/current_capability.rst b/docs/imexam/current_capability.rst
@@ -151,7 +151,8 @@ but not yet fully implemented should return an error to that affect.
 
 
 **load_fits**\ (fname="", extver=1, extname=None):
-    Load a fits image into the current frame
+    Load a fits image into the current frame.
+    fname can be a filename or a fits HDU
 
 
 **load_mef_as_cube**\ (filename=None):

diff --git a/docs/imexam/description.rst b/docs/imexam/description.rst
@@ -268,7 +268,7 @@ If you are having display issues, some build problems may exist with the depende
 
   backend: Qt4Agg
 
-The package works with the Qt5Agg and notebook backends, but on occasion I've seen the matplotlib window take two cycles to update, especially inside the Jupyter notebook with inline plots, meaning you may have to hit the exam key twice for the plot to appear. This issue still needs to be worked out, if you're running into it try using the Qt4Agg backend or plotting outside the notebook and saving the figures through the imexam grab or save calls.
+The package works with the Qt5Agg and notebook backends, but on occasion I've seen the matplotlib window take two cycles to update, especially inside the Jupyter notebook with inline plots, meaning you may have to hit the exam key twice for the plot to appear. This issue still needs to be worked out, if you're running into it try using the Qt4Agg backend or plotting outside the notebook and saving the figures through the imexam grab or save calls. More information about the backends for matplotlib can be found here: https://matplotlib.org/users/shell.html
 
 
 If you get an error about not finding the file "import" when you use the grab() function to save a copy of the DS9 window.

diff --git a/docs/imexam/example5.rst b/docs/imexam/example5.rst
@@ -25,13 +25,13 @@ These are the functions you now have access to:
 
         plots.aper_phot                 plots.contour_plot              plots.histogram_plot            plots.plot_line                 plots.set_colplot_pars          plots.set_surface_pars
         plots.aperphot_def_pars         plots.curve_of_growth_def_pars  plots.imexam_option_funcs       plots.plot_name                 plots.set_column_fit_pars       plots.show_xy_coords
-        plots.aperphot_pars             plots.curve_of_growth_pars      plots.line_fit                  plots.print_options             plots.set_contour_pars          plots.showplt
+        plots.aperphot_pars             plots.curve_of_growth_pars      plots.line_fit                  plots.print_options             plots.set_contour_pars          plots.set_plot_name
         plots.colplot_def_pars          plots.curve_of_growth_plot      plots.line_fit_def_pars         plots.register                  plots.set_data                  plots.sleep_time
         plots.colplot_pars              plots.do_option                 plots.line_fit_pars             plots.report_stat               plots.set_histogram_pars        plots.surface_def_pars
         plots.column_fit                plots.gauss_center              plots.lineplot_def_pars         plots.report_stat_def_pars      plots.set_line_fit_pars         plots.surface_pars
         plots.column_fit_def_pars       plots.get_options               plots.lineplot_pars             plots.report_stat_pars          plots.set_lineplot_pars         plots.surface_plot
         plots.column_fit_pars           plots.get_plot_name             plots.new_plot_window           plots.reset_defpars             plots.set_option_funcs          plots.unlearn_all
-        plots.contour_def_pars          plots.histogram_def_pars        plots.option_descrip            plots.save_figure               plots.set_plot_name
+        plots.contour_def_pars          plots.histogram_def_pars        plots.option_descrip            plots.save_figure               
         plots.contour_pars              plots.histogram_pars            plots.plot_column               plots.set_aperphot_pars         plots.set_radial_pars
 
 

diff --git a/imexam/_astropy_init.py b/imexam/_astropy_init.py
@@ -119,5 +119,5 @@ def test(package=None, test_path=None, args=None, plugins=None,
                             "importing from source, this is expected.")
                     warn(config.configuration.ConfigurationDefaultMissingWarning(wmsg))
                     del e
-                except:
+                except Exception:
                     raise orig_error
diff --git a/imexam/connect.py b/imexam/connect.py
@@ -232,22 +232,40 @@ def _run_imexam(self):
                 self._check_frame()
                 if self.window.iscube():
                     self._check_slice()
+
+                # This loop now recognizes the arrow keys
+                # for moving the cursor in the window, it calls
+                # the windows cursor function. However, depending
+                # on how the use has their windowing focus setup
+                # they might loose focus on the DS9 window and have to
+                # move the cursor to gain focus again, is there a way
+                # around this? Cursor is not implemented in the ginga
+                # interface.
                 try:
                     x, y, current_key = self.readcursor()
-                    self._check_frame()
-                    if self.window.iscube():
-                        self._check_slice()
-                    if current_key not in keys and 'q' not in current_key:
-                        print("Invalid key")
-                        self.exam._close_plots()
+                    if current_key in ["Left", "Right", "Up", "Down"]:
+                        if current_key == "Left":
+                            x, y = x - 1, y
+                        if current_key == "Right":
+                            x, y = x + 1, y
+                        if current_key == "Down":
+                            x, y = x, y - 1
+                        if current_key == "Up":
+                            x, y = x, y + 1
+                        self.cursor(x=x, y=y)
                     else:
-                        if 'q' in current_key:
-                            current_key = None
+                        if current_key not in keys and 'q' not in current_key:
                             self.exam._close_plots()
                         else:
-                            self.exam.do_option(
-                                x, y, current_key)
-
+                            if 'q' in current_key:
+                                current_key = None
+                                self.exam._close_plots()
+                            else:
+                                self._check_frame()
+                                if self.window.iscube():
+                                    self._check_slice()
+                                self.exam.do_option(
+                                    x, y, current_key)
                 except KeyError:
                     print(
                         "Invalid key, use\n: {0}".format(

diff --git a/imexam/ginga_viewer.py b/imexam/ginga_viewer.py
@@ -563,12 +563,12 @@ def embed(self, width=600, height=650):
 
         return self.ginga_view.embed(width, height)
 
-    def load_fits(self, fname="", extver=None):
+    def load_fits(self, fname=None, extver=None):
         """Load fits image to current frame.
 
         Parameters
         ----------
-        fname: string, optional
+        fname: string, FITS HDU
             The name of the file to be loaded. You can specify the full
             extension in the name, such as
             filename_flt.fits[sci,1] or filename_flt.fits[1]
@@ -582,38 +582,57 @@ def load_fits(self, fname="", extver=None):
         number, not the version number associated with a name
         """
         if fname is None:
-            raise ValueError("No filename provided")
+            raise ValueError("No filename or HDU provided")
 
-        try:
-            shortname, extn, extv = util.verify_filename(fname)
-            image = AstroImage(logger=self.logger)
+        if isinstance(fname, (fits.hdu.image.PrimaryHDU, fits.hdu.image.ImageHDU)):
+            # Simple fits, data + header
+            shortname = fname
+            extn = None
+            if extver is None:
+                extv = None
+                extver = 0
+
+        elif isinstance(fname, fits.hdu.hdulist.HDUList):
+            shortname = fname
+            extn = None
+            extv = extver
 
+        elif isinstance(fname, str):
+            shortname, extn, extv = util.verify_filename(fname)
             if extn is not None:
-                raise ValueError("Extension name given, must specify "
-                                 "the absolute extension you want")
-            # prefer specified over filename
+                raise ValueError("Extension name given, must "
+                                 "specify the absolute extension you want")
+            # prefer the keyword value over the extension in the name
             if extver is None:
                 extver = extv
 
-            if (extv is None and extver is None):
-                mef_file, nextend, first_image = util.check_valid(shortname)
-                # if mef_file:
-                #     extver = 1  # MEF fits
-                # else:
-                #     extver = 0  # simple fits
-                extver = first_image  # really ext number for first IMAGE
+        else:
+            raise TypeError("Expected FITS data as input")
 
-            with fits.open(shortname) as filedata:
-                hdu = filedata[extver]
-                image.load_hdu(hdu)
+        # safety for a valid imexam file
+        if ((extv is None) and (extver is None)):
+            mef_file, nextend, first_image = util.check_valid(shortname)
+            extver = first_image  # the extension of the first IMAGE
 
+        image = AstroImage(logger=self.logger)
+
+        try:
+            if isinstance(fname, str):
+                with fits.open(shortname) as filedata:
+                    hdu = filedata[extver]
+                    image.load_hdu(hdu)
+            else:
+                if extver:
+                    hdu = shortname[extver]
+                else:
+                    hdu = shortname
+                image.load_hdu(hdu)
+            self._set_frameinfo(fname=shortname, hdu=hdu, image=image)
+            self.ginga_view.set_image(image)
         except Exception as e:
-            self.logger.error("Exception opening file: {0}".format(repr(e)))
+            self.logger.error("Exception loading image: {0}".format(repr(e)))
             raise Exception(repr(e))
 
-        self._set_frameinfo(fname=shortname, hdu=hdu, image=image)
-        self.ginga_view.set_image(image)
-
     def panto_image(self, x, y):
         """Change to x,y  physical image coordinates.
 

diff --git a/imexam/imexam_defpars.py b/imexam/imexam_defpars.py
@@ -131,7 +131,7 @@
                 "floor": [None, "Minimum value to be contoured"],
                 "ceiling": [None, "Maximum value to be contoured"],
                 "ncontours": [8, "Number of contours to be drawn"],
-                "linestyle": ["--", "matplotlib linestyle"],
+                "linestyles": ["--", "matplotlib linestyle"],
                 "label": [True, "Label major contours with their values? [bool]"],
                 "cmap": ["viridis", "Colormap (matplotlib style) for image"],
                 }