Merge pull request #330 from nmearl/master

CubeViz infrastructure refactor

.travis.yml

@@ -32,13 +32,15 @@ env:
         - ASTROPY_VERSION=stable
         - MAIN_CMD='python setup.py'
         - SETUP_CMD='test'
+        - PIP_DEPENDENCIES=''
         - EVENT_TYPE='pull_request push'
 
-
-        # List other runtime dependencies for the package that are available as
-        # conda packages here.
+
+        # For this package-template, we include examples of Cython modules,
+        # so Cython is required for testing. If your package does not include
+        # Cython code, you can set CONDA_DEPENDENCIES=''
         - CONDA_DEPENDENCIES='pyqt'
-        
+
         # List other runtime dependencies for the package that are available as
         # pip packages here.
         - PIP_DEPENDENCIES='scipy specutils<=0.2.2 six pyyaml pyqtgraph qtpy py_expression_eval sphinx_rtd_theme sphinx_automodapi'
@@ -78,19 +80,16 @@ matrix:
         # Check for sphinx doc build warnings - we do this first because it
         # may run for a long time
         - os: linux
-          env: SETUP_CMD='build_docs -w'
+          env: SETUP_CMD='build_docs -w' SPHINX_VERSION='<1.6'
 
-        # Now try Astropy dev and LTS vesions with the latest 3.x and 2.7.
-        - os: linux
-          env: PYTHON_VERSION=2.7 ASTROPY_VERSION=development
-               EVENT_TYPE='pull_request push cron'
+        # Now try Astropy dev with the latest Python and LTS with Python 2.7 and 3.x.
         - os: linux
           env: ASTROPY_VERSION=development
                EVENT_TYPE='pull_request push cron'
         - os: linux
-          env: PYTHON_VERSION=2.7 ASTROPY_VERSION=lts NUMPY_VERSION=1.12
+          env: PYTHON_VERSION=2.7 ASTROPY_VERSION=lts
         - os: linux
-          env: ASTROPY_VERSION=lts NUMPY_VERSION=1.12
+          env: ASTROPY_VERSION=lts
 
         # Try all python versions and Numpy versions. Since we can assume that
         # the Numpy developers have taken care of testing Numpy with different
@@ -103,15 +102,17 @@ matrix:
           env: PYTHON_VERSION=3.4 NUMPY_VERSION=1.10
         - os: linux
           env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.11
+        - os: linux
+          env: NUMPY_VERSION=1.12
 
         # Try numpy pre-release
         - os: linux
           env: NUMPY_VERSION=prerelease
                EVENT_TYPE='pull_request push cron'
 
-#        # Do a PEP8 test with pycodestyle
-#        - os: linux
-#          env: MAIN_CMD='pycodestyle specviz --count' SETUP_CMD=''
+        # Do a PEP8 test with pycodestyle
+        - os: linux
+          env: MAIN_CMD='pycodestyle specviz --count' SETUP_CMD=''
 
     allow_failures:
         # Do a PEP8 test with pycodestyle
@@ -132,7 +133,7 @@ install:
     # in how to install a package, in which case you can have additional
     # commands in the install: section below.
 
-    - git clone git://github.com/astropy/ci-helpers.git
+    - git clone --depth 1 git://github.com/astropy/ci-helpers.git
     - source ci-helpers/travis/setup_conda.sh
 
     # As described above, using ci-helpers, you should be able to set up an

docs/api.rst

@@ -17,7 +17,12 @@ Data Objects
 
 Object Event Handling
 ^^^^^^^^^^^^^^^^^^^^^
-.. automodapi:: specviz.core.comms
+.. automodapi:: specviz.core.events
+   :no-heading:
+
+Object Dispatch Machinery
+^^^^^^^^^^^^^^^^^^^^^^^^^
+.. automodapi:: specviz.core.dispatch
    :no-heading:
 
 Spectrum Layer Plotting

setup.py

@@ -99,7 +99,7 @@
     PACKAGENAME, [os.path.normpath(
         os.path.join("data", os.path.relpath(x[0], root_dir), "*"))
                   for x in os.walk(root_dir)])
-package_info['package_data'][PACKAGENAME].append('external/glue/*.ui')
+package_info['package_data'][PACKAGENAME].append('third_party/glue/*.ui')
 
 # Define entry points for command-line scripts
 entry_points = {'console_scripts': []}

specviz/analysis/models/blackbody.py

@@ -4,7 +4,7 @@
 
 from astropy.modeling import Fittable1DModel
 from astropy.modeling.parameters import Parameter
-from astropy.analytic_functions import blackbody_lambda
+from astropy.modeling.blackbody import blackbody_lambda
 
 __all__ = ['BlackBody']
 

specviz/analysis/utils.py

@@ -35,7 +35,7 @@ def resample(data_in, x_in, x_out, y, data_out=None, kind='linear'):
     array([(4100, 1.0, 1.0), (4300, 1.0, 1.0), (4500, 1.0, 1.0)],
           dtype=[('wlen', '<i8'), ('flux', '<f8'), ('ivar', '<f8')])
 
-    The input grid can also be external to the structured array of spectral
+    The input grid can also be third_party to the structured array of spectral
     data, for example:
 
     >>> data = np.ones((5,), [('flux', float), ('ivar', float)])

specviz/app.py

@@ -29,7 +29,7 @@
 from docopt import docopt
 
 from .widgets.utils import ICON_PATH
-from .core.comms import dispatch
+from .core.events import dispatch
 from .widgets.windows import MainWindow
 
 try:
@@ -40,7 +40,12 @@
 
 
 class App(object):
-    def __init__(self, hide_plugins=False):
+    def __init__(self, hidden=None, disabled=None):
+        hidden = hidden or {}
+        disabled = disabled or {}
+
+        self._instanced_plugins = {}
+
         # Instantiate main window object
         self._all_tool_bars = {}
 
@@ -53,52 +58,54 @@ def __init__(self, hide_plugins=False):
         # self.main_window.setDockNestingEnabled(True)
 
         # Load system and user plugins
-        self.load_plugins(hidden=hide_plugins)
+        self.load_plugins(hidden=hidden, disabled=disabled)
 
         # Setup up top-level connections
         self._setup_connections()
 
         # Parse arguments
-        args = docopt(__doc__, version=version)
-        self._parse_args(args)
+        try:
+            args = docopt(__doc__, version=version)
+        except SystemExit:
+            logging.error("Received unknown command line arguments.")
+        else:
+            self._parse_args(args)
 
     def _parse_args(self, args):
         if args.get("load", False):
             file_filter = args.get("--loader", "Auto (*)")
             dispatch.on_file_read.emit(args.get("<path>"),
                                        file_filter=file_filter)
 
-    def load_plugins(self, hidden=False):
+    def load_plugins(self, hidden=None, disabled=None):
         from .interfaces.registries import plugin_registry
 
-        instance_plugins = [x() for x in plugin_registry.members]
+        self._instanced_plugins = {
+            x.name:x() for x in plugin_registry.members
+            if not disabled.get(x.name, False)}
 
-        for instance_plugin in sorted(instance_plugins,
+        for inst_plgn in sorted(self._instanced_plugins.values(),
                                       key=lambda x: x.priority):
-            if instance_plugin.location != 'hidden':
-                if instance_plugin.location == 'right':
+            if inst_plgn.location != 'hidden':
+                if inst_plgn.location == 'right':
                     location = Qt.RightDockWidgetArea
-                elif instance_plugin.location == 'top':
+                elif inst_plgn.location == 'top':
                     location = Qt.TopDockWidgetArea
                 else:
                     location = Qt.LeftDockWidgetArea
 
-                self.main_window.addDockWidget(location, instance_plugin)
+                self.main_window.addDockWidget(location, inst_plgn)
 
-                if hidden:
-                    instance_plugin.hide()
+                if hidden.get(inst_plgn.name):
+                    inst_plgn.hide()
 
                 # Add this dock's visibility action to the menu bar
                 self.menu_docks.addAction(
-                    instance_plugin.toggleViewAction())
-
-        # Resize the widgets now that they are all present
-        for ip in instance_plugins[::-1]:
-            ip.setMinimumSize(ip.sizeHint())
-        #     QApplication.processEvents()
+                    inst_plgn.toggleViewAction())
 
         # Sort actions based on priority
-        all_actions = [y for x in instance_plugins for y in x._actions]
+        all_actions = [y for x in self._instanced_plugins.values()
+                       for y in x._actions]
         all_categories = {}
 
         for act in all_actions:
@@ -134,16 +141,6 @@ def _get_tool_bar(self, name, priority):
             tool_bar.setToolButtonStyle(Qt.ToolButtonTextUnderIcon)
             tool_bar.setMovable(False)
 
-            tool_bar.setStyleSheet("""
-                QToolBar {
-                    icon-size: 32px;
-                }
-
-                QToolBar QToolButton {
-                    height: 48px;
-                }
-            """)
-
             self._all_tool_bars[name] = dict(widget=tool_bar,
                                              priority=int(priority),
                                              name=name)
@@ -219,7 +216,7 @@ def glue_setup():
         raise Exception("glue 0.10.2 or later is required for the specviz "
                         "plugin")
 
-    from .external.glue.data_viewer import SpecVizViewer
+    from .third_party.glue.data_viewer import SpecVizViewer
     from glue.config import qt_client
     qt_client.add(SpecVizViewer)
 

specviz/core/__init__.py

@@ -1 +1 @@
-from .comms import dispatch, DispatchHandle
+from .events import dispatch

specviz/core/data.py

@@ -4,13 +4,11 @@
 from __future__ import (absolute_import, division, print_function,
                         unicode_literals)
 
-# STDLIB
 import logging
 import re
 
-# THIRD-PARTY
 import numpy as np
-from astropy.units import Quantity, LogQuantity, LogUnit, spectral_density, spectral
+from astropy.units import Quantity, LogQuantity, LogUnit, spectral_density, spectral, Unit
 from py_expression_eval import Parser
 
 # FIXME: the latest developer version of Astropy removes OrderedDict which is needed by
@@ -21,6 +19,7 @@
 utils.OrderedDict = OrderedDict
 
 from specutils.core.generic import Spectrum1DRef
+from astropy.nddata import StdDevUncertainty
 
 logging.basicConfig(level=logging.INFO)
 
@@ -50,6 +49,7 @@ def _make_quantity(data, unit):
     else:
         return Quantity(data, unit=unit)
 
+
 class Spectrum1DRefLayer(Spectrum1DRef):
     """
     Class to handle layers in SpecViz.
@@ -72,15 +72,21 @@ class Spectrum1DRefLayer(Spectrum1DRef):
         Arguments passed to the
         `~spectutils.core.generic.Spectrum1DRef` object.
     """
-    def __init__(self, data, wcs=None, parent=None, layer_mask=None, *args,
-                 **kwargs):
-        super(Spectrum1DRefLayer, self).__init__(data, wcs=wcs, *args,
-                                                 **kwargs)
+    def __init__(self, data, wcs=None, parent=None, layer_mask=None,
+                 uncertainty=None, unit=None, mask=None, *args,**kwargs):
+        uncertainty = StdDevUncertainty(np.zeros(data.shape)) if uncertainty is None else uncertainty
+        unit = unit or Unit('')
+        mask = mask if mask is not None else np.zeros(data.shape).astype(bool)
+
+        super(Spectrum1DRefLayer, self).__init__(data, wcs=wcs, unit=unit,
+                                                 uncertainty=uncertainty,
+                                                 mask=mask,
+                                                 *args,**kwargs)
         self._parent = parent
         self._layer_mask = layer_mask
 
     @classmethod
-    def from_parent(cls, parent, layer_mask=None, name=None):
+    def from_parent(cls, parent, layer_mask=None, name=None, copy=True):
         """
         Create a duplicate child layer from a parent layer
 
@@ -107,7 +113,7 @@ def from_parent(cls, parent, layer_mask=None, name=None):
                    dispersion=parent.dispersion,
                    dispersion_unit=parent.dispersion_unit,
                    layer_mask=layer_mask, parent=parent, meta=parent.meta,
-                   copy=False)
+                   copy=copy)
 
     def from_self(self, name="", layer_mask=None):
         """
@@ -126,10 +132,8 @@ def from_self(self, name="", layer_mask=None):
         new_layer:
             The new, parentless, layer.
         """
-        gen_spec = Spectrum1DRef.copy(self, name=name)
-
         return self.from_parent(
-            parent=gen_spec, layer_mask=layer_mask, name=name
+            parent=self._parent, layer_mask=layer_mask, name=name, copy=True
         )
 
     @classmethod
@@ -302,40 +306,32 @@ def _evaluate(cls, layers, formula):
             formula = formula.replace(layer.name,
                                       layer.name.replace(" ", "_"))
 
+        layer_vars = {layer.name.replace(" ", "_"):layer
+                      for layer in layers}
+
         try:
             expr = parser.parse(formula)
         except Exception as e:
             logging.error(e)
             return
 
         # Extract variables
-        vars = expr.variables()
+        expr_vars = expr.variables()
 
-        # List the models in the same order as the variables
-        # sorted_layers = [next(l for v in vars for l in layers
-        #                       if l.name.replace(" ", "_") == v)]
-        # sorted_layers = [l for v in vars for l in layers
-        #                  if l.name.replace(" ", "_") == v]
-        sorted_layers = []
-
-        for v in vars:
-            for l in layers:
-                if l.name.replace(" ", "_") == v:
-                    sorted_layers.append(l)
-                    break
-
-        if len(sorted_layers) != len(vars):
-            logging.error("Incorrect layer arithmetic formula: the number "
-                          "of layers does not match the number of variables.")
+        # Get the union of the sets of variables listed in the expression and
+        # layer names of the current layer list
+        union_set = set(layer_vars.keys()).union(set(expr_vars))
+
+        if len(union_set) != 0:
+            logging.error("Mis-match between current layer list and expression:"
+                          "%s", union_set)
 
         try:
-            result = parser.evaluate(expr.simplify({}).toString(),
-                                     dict(pair for pair in
-                                          zip(vars, sorted_layers)))
-            result._dispersion = sorted_layers[0]._dispersion
-            result.dispersion_unit = sorted_layers[0].dispersion_unit
+            result = parser.evaluate(expr.simplify({}).toString(), layer_vars)
+            result = result.__class__.copy({'dispersion': layers[0].dispersion,
+                                            'dispersion_unit': layers[0].dispersion_unit})
         except Exception as e:
-            logging.error("While evaluating formula: {}".format(e))
+            logging.error("While evaluating formula: %s", e)
             return
 
         return result