Merge pull request #148 from nmearl/specviz-interop

[WIP] Embed SpecViz 1D viewer in MOSViz

.gitignore

@@ -59,3 +59,4 @@ distribute-*.tar.gz
 
 # Mac OSX
 .DS_Store
+.vscode/settings.json

.rtd-environment.yml

@@ -11,3 +11,4 @@ dependencies:
   - glue-core>=0.13.0
   - qtpy
   - nomkl
+  - specviz>=0.5

.travis.yml

@@ -40,7 +40,7 @@ env:
 
         # List other runtime dependencies for the package that are available as
         # pip packages here.
-        - PIP_DEPENDENCIES='sphinx_rtd_theme sphinx_automodapi qtpy codecov regions>=0.3'
+        - PIP_DEPENDENCIES='sphinx_rtd_theme sphinx_automodapi qtpy codecov regions>=0.3 specviz>=0.6.2'
 
         # Conda packages for affiliated packages are hosted in channel
         # "astropy" while builds for astropy LTS with recent numpy versions
@@ -88,7 +88,7 @@ matrix:
         # time.
 
         - os: linux
-          env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.11
+          env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.11 ASTROPY_VERSION=3.0
 
         # Try numpy pre-release
         - os: linux

docs/installation.rst

@@ -2,19 +2,19 @@
 Installation
 ************
 
-MOSViz is packaged in the Conda environment system and therefore 
-requires Miniconda to be installed. This makes it reasonably simple 
-to install MOSViz along with all its dependencies.
-
-If you do not have Miniconda, please follow the `instructions here
-<https://conda.io/miniconda.html>`_ to install it, or scroll down for
-manual installation of MOSViz.
+MOSViz is packaged and distributed through both Anaconda via the GlueViz
+channel, as well as through the Python Package Index (PyPI). It is also
+available from source.
 
 
 Install via Conda
 -----------------
 
-Once you have Miniconda installed, then all you have to do to install MOSViz is
+In order to use the Anaconda package, you must first install an
+Anaconda distribution. If you do not have Anaconda, please follow the
+`instructions here <https://www.anaconda.com/download>`_ to install it.
+
+Once you have Anaconda installed, all you have to do to install MOSViz is
 simply type the following at any Bash terminal prompt::
 
     $ conda create -n <environment_name> -c glueviz mosviz
@@ -27,6 +27,19 @@ To launch MOSViz now you enter::
 
     $ mosviz
 
+
+Install via PyPI
+----------------
+
+To install MOSViz using PyPI type the following at any terminal prompt::
+
+    $ pip install mosviz
+
+You will also need to install the PyQt package as well by typing the following::
+
+    $ pip install pyqt5
+
+
 Install via source
 ------------------
 
@@ -61,6 +74,7 @@ Or, have the `pip <http://pip.pypa.org>`_ package manager do everything for you:
 Either way, the MosView Viewer should show up in the list of available Glue
 viewers.
 
+
 SpecViz functionality
 ---------------------
 

mosviz/cli.py

@@ -93,5 +93,4 @@ def main(argv=sys.argv):
         ga.add_datasets(data_collection, datasets, auto_merge=False)
 
     ga.run_startup_action('mosviz')
-
-    sys.exit(ga.start(maximized=True))
+    ga.start(maximized=True)

mosviz/loaders/deimos_loaders.py

@@ -21,17 +21,21 @@ def deimos_spectrum1D_reader(file_name):
     along with their Wavelength and Inverse Variance
     arrays.
     """
-    hdulist = fits.open(file_name)
-    data = Data(label='1D Spectrum')
-    data.header = hdulist[1].header
+    with fits.open(file_name) as hdulist:
+        data = Data(label='1D Spectrum')
+        hdulist[1].header['CTYPE1'] = 'WAVE'
+        hdulist[1].header['CUNIT1'] = 'Angstrom'
+        data.header = hdulist[1].header
+        wcs = WCS(hdulist[1].header)
+        data.coords = coordinates_from_wcs(wcs)
 
-    full_wl = np.append(hdulist[1].data['LAMBDA'][0], hdulist[2].data['LAMBDA'][0])
-    full_spec = np.append(hdulist[1].data['SPEC'][0], hdulist[2].data['SPEC'][0])
-    full_ivar = np.append(hdulist[1].data['IVAR'][0], hdulist[2].data['IVAR'][0])
+        full_wl = np.append(hdulist[1].data['LAMBDA'][0], hdulist[2].data['LAMBDA'][0])
+        full_spec = np.append(hdulist[1].data['SPEC'][0], hdulist[2].data['SPEC'][0])
+        full_ivar = np.append(hdulist[1].data['IVAR'][0], hdulist[2].data['IVAR'][0])
 
-    data.add_component(full_wl, 'Wavelength')
-    data.add_component(full_spec, 'Flux')
-    data.add_component(1 / np.sqrt(full_ivar), 'Uncertainty')
+        data.add_component(full_wl, 'Wavelength')
+        data.add_component(full_spec, 'Flux')
+        data.add_component(1 / np.sqrt(full_ivar), 'Uncertainty')
 
     return data
 
@@ -45,14 +49,17 @@ def deimos_spectrum2D_reader(file_name):
     Wavelength information comes from the WCS.
     """
 
-    hdulist = fits.open(file_name)
-    data = Data(label='2D Spectrum')
-    hdulist[1].header['CTYPE2'] = 'Spatial Y'
-    wcs = WCS(hdulist[1].header)
-    # original WCS has both axes named "LAMBDA", glue requires unique component names
+    with fits.open(file_name) as hdulist:
+        data = Data(label='2D Spectrum')
+        hdulist[1].header['CTYPE1'] = 'WAVE'
+        hdulist[1].header['CUNIT1'] = 'Angstrom'
+        hdulist[1].header['CTYPE2'] = 'Spatial Y'
+        wcs = WCS(hdulist[1].header)
+        # original WCS has both axes named "LAMBDA", glue requires unique component names
+
+        data.coords = coordinates_from_wcs(wcs)
+        data.header = hdulist[1].header
+        data.add_component(hdulist[1].data['FLUX'][0], 'Flux')
+        data.add_component(1 / np.sqrt(hdulist[1].data['IVAR'][0]), 'Uncertainty')
 
-    data.coords = coordinates_from_wcs(wcs)
-    data.header = hdulist[1].header
-    data.add_component(hdulist[1].data['FLUX'][0], 'Flux')
-    data.add_component(1 / np.sqrt(hdulist[1].data['IVAR'][0]), 'Uncertainty')
     return data

mosviz/loaders/loader_selection.py

@@ -228,26 +228,29 @@ def _validation_checks(self, *args, **kwargs):
             loader = loaders[loader_name]
             column_name = getattr(self, column)
             filenames = self.data.get_component(column_name).labels
+            path = os.sep.join(
+                self.data._load_log.path.split(os.sep)[:-1])
 
             test_filename = "None"
             for filename in filenames:
+                file_path = os.path.join(path, filename)
                 if os.path.basename(filename) != "None":
                     test_filename = filename
                     break
 
             if test_filename == "None":
                 continue
-
             try:
-                loader(test_filename)
-            except Exception as e:
+                loader(file_path)
+
+                self.validate(True, "All spectra and cutout files exist and "
+                              "the loaders are able to read in the first one "
+                              "of each.")
+            except:
                 self.validate(False, "An error occurred when trying to read in "
                               "'{0}' using the loader '{1}' (see terminal for "
                               "the full error).".format(filenames[0], loader_name))
-                print(e)
-
-        self.validate(True, "All spectra and cutout files exist and the loaders "
-                      "are able to read in the first one of each.")
+                return
 
     def validate(self, valid, message):
         if valid: