Fix intersphinx

docs/conf.py

@@ -173,7 +173,13 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/', None),
+    'numpy': ('http://numpy.readthedocs.io/en/latest/', None),
+    'pyside': ('https://srinikom.github.io/pyside-docs/', None),
+    'pyqt5': ('http://pyqt.sourceforge.net/Docs/PyQt5/', None),
+    'ginga': ('http://ginga.readthedocs.io/en/latest/', None),
+}
 
 import sphinx_rtd_theme
 html_theme = "sphinx_rtd_theme"

pdsspect/basic.py

@@ -74,13 +74,13 @@ class Basic(QtWidgets.QDialog, PDSSpectImageSetViewBase):
         Canvas to view the image
     controller : :class:`BasicController`
         Controller for view
-    image_menu : :class:`QtWidgets.QComboBox`
+    image_menu : :class:`QtWidgets.QComboBox <PySide.QtGui.QComboBox>`
         Drop down menu to pick the current image
     histogram : :class:`~.histogram.HistogramModel`
         Model for the :attr:`histogram_widget`
     histogram_widget : :class:`BasicHistogramWidget`
         The histogram widget to adjust the cut levels
-    layout : :class:`QtWidgets.QVBoxLayout`
+    layout : :class:`QtWidgets.QVBoxLayout <PySide.QtGui.QVBoxLayout>`
         The main layout
     """
 

pdsspect/histogram.py

@@ -160,7 +160,7 @@ def register(self, view):
 
         Parameters
         ----------
-        view : :class:`QtWidgets.QWidget`
+        view : :class:`QtWidgets.QWidget <PySide.QtGui.QWidget>`
             A view that utilizes this model
         """
         self._views.add(view)
@@ -170,7 +170,7 @@ def unregister(self, view):
 
         Parameters
         ----------
-        view : :class:`QtWidgets.QWidget`
+        view : :class:`QtWidgets.QWidget <PySide.QtGui.QWidget>`
             A view that utilizes this model
         """
         self._views.remove(view)

pdsspect/pan_view.py

@@ -35,7 +35,7 @@ def add_ROI(self, coordinates):
 
         Parameters
         ----------
-        coordinates : :class:`np.ndarray` or :obj:`tuple`
+        coordinates : :class:`numpy.ndarray` or :obj:`tuple`
             Either a ``(m x 2)`` array or a tuple of two arrays
 
             If an array, the first column are the x coordinates and the second
@@ -53,7 +53,7 @@ def erase_ROI(self, coordinates):
 
         Parameters
         ----------
-        coordinates : :class:`np.ndarray` or :obj:`tuple`
+        coordinates : :class:`numpy.ndarray` or :obj:`tuple`
             Either a ``(m x 2)`` array or a tuple of two arrays
 
             If an array, the first column are the x coordinates and the second
@@ -82,7 +82,7 @@ class PanView(QtWidgets.QWidget, PDSSpectImageSetViewBase):
         The view's controller
     parent : None
         The view's parent
-    main_layout : :class:`QtWidgets.QVBoxLayout`
+    main_layout : :class:`QtWidgets.QVBoxLayout <PySide.QtGui.QVBoxLayout>`
         The main layout of the view
     view_canvas : :class:`~pdsspect.pds_image_view_canvas.PDSImageViewCanvas`
         Canvas to view the image

pdsspect/pds_image_view_canvas.py

@@ -24,7 +24,7 @@ def add_subview(self, subview):
         Raises
         ------
         TypeError
-            When subview is an and :class:`ImageViewCanvas` object
+            When subview is not an :class:`ImageViewCanvas` object
         """
 
         if not isinstance(subview, ImageViewCanvas):

pdsspect/pdsspect.py

@@ -28,24 +28,24 @@ class PDSSpect(QtWidgets.QMainWindow, PDSSpectImageSetViewBase):
         The main viewer for panning
     pan_view : :class:`~.pdsspect.pan_view.PanView`
         The view in which the user makes ROI selections
-    selection_btn : :class:`~QtWidgets.QPushButton`
+    selection_btn : :class:`~QtWidgets.QPushButton <PySide.QtGui.QPushButton>`
         Button to open the selections window
     selection_window : :class:`Selection`
         The selection window to adjust ROI, import ROIs, and export ROIs
-    basic_btn : :class:`~QtWidgets.QPushButton`
+    basic_btn : :class:`~QtWidgets.QPushButton <PySide.QtGui.QPushButton>`
         Button to open the basic window
     basic_window : :class:`Basic`
         Window to adjust cut levels and change images
-    transforms_btn : :class:`QtWidgets.QPushButton`
+    transforms_btn : :class:`QtWidgets.QPushButton <PySide.QtGui.QPushButton>`
         Open Transforms window
     transforms_window : :class:`Transforms`
         Window to flip x axis, flip y axis, or switch x and y axis
-    quit_btn : :class:`~QtWidgets.QPushButton`
+    quit_btn : :class:`~QtWidgets.QPushButton <PySide.QtGui.QPushButton>`
         Quit
-    button_layout : :class:`~QtWidgets.QHBoxLayout`
+    button_layout : :class:`~QtWidgets.QHBoxLayout <PySide.QtGui.QHBoxLayout>`
         Layout for the buttons. If you want to re-adjust where the buttons
         go, override this attribute
-    main_layout : :class:`~QtWidgets.QVBoxLayout`
+    main_layout : :class:`~QtWidgets.QVBoxLayout <PySide.QtGui.QVBoxLayout>`
         Place the image viewer over the buttons. Overide this attribute if
         changing overall layout
     """

pdsspect/pdsspect_image_set.py

@@ -355,8 +355,8 @@ def center(self, new_center):
 
     @property
     def all_rois_coordinates(self):
-        """:obj:`tuple` of two :class:`np.ndarray` : Coordinates of where there
-        is a pixel selected in a ROI
+        """:obj:`tuple` of two :class:`numpy.ndarray` : Coordinates of where
+        there is a pixel selected in a ROI
         """
         return np.where((self._roi_data != 0).any(axis=2))
 
@@ -444,19 +444,19 @@ def edges(self):
 
     @property
     def pan_slice(self):
-        """:class:`np.s_` : A slice of the pan to extract data from an array"""
+        """:obj:`numpy.s_` : Slice of pan to extract data from an array"""
         x1, y1, x2, y2 = self.edges
         pan_slice = np.s_[y1:y2:1, x1:x2:1]
         return pan_slice
 
     @property
     def pan_data(self):
-        """:class:`np.ndarray` : The data within the pan"""
+        """:class:`numpy.ndarray` : The data within the pan"""
         return self.current_image.get_data()[self.pan_slice]
 
     @property
     def pan_roi_data(self):
-        """:class:`np.ndarray` : The ROI data in the pan"""
+        """:class:`numpy.ndarray` : The ROI data in the pan"""
         return self._roi_data[self.pan_slice]
 
     def _get_rgb255_from_color(self, color):
@@ -498,7 +498,7 @@ def _erase_coords(self, coordinates):
 
         Parameters
         ----------
-        coordinates : :class:`np.ndarray` or :obj:`tuple`
+        coordinates : :class:`numpy.ndarray` or :obj:`tuple`
             Either a ``(m x 2)`` array or a tuple of two arrays
 
             If an array, the first column are the x coordinates and the second
@@ -515,7 +515,7 @@ def add_coords_to_roi_data_with_color(self, coordinates, color):
 
         Parameters
         ----------
-        coordinates : :class:`np.ndarray` or :obj:`tuple`
+        coordinates : :class:`numpy.ndarray` or :obj:`tuple`
             Either a ``(m x 2)`` array or a tuple of two arrays
 
             If an array, the first column are the x coordinates and the second
@@ -558,7 +558,7 @@ def get_coordinates_of_color(self, color):
 
         Returns
         -------
-        coordinates : :obj:`tuple` of two :class:`np.ndarray`
+        coordinates : :obj:`tuple` of two :class:`numpy.ndarray`
             The first array are the x coordinates and the second are the
             corresponding y coordinates
         """

pdsspect/pdsspect_view.py

@@ -58,12 +58,12 @@ class PDSSpectView(QtWidgets.QWidget, PDSSpectImageSetViewBase):
     image_set : :class:`~.pdsspect_image_set.PDSSpectImageSet`
         pdsspect model
     controller : :class:`PDSSpectViewController`
-    main_layout : :class:`QtWidgets.QVBoxLayout`
-    zoom_layout : :class:`QtWidgets.QHBoxLayout`
+    main_layout : :class:`QtWidgets.QVBoxLayout <PySide.QtGui.QVBoxLayout>`
+    zoom_layout : :class:`QtWidgets.QHBoxLayout <PySide.QtGui.QHBoxLayout>`
         Layout for :attr:`zoom_label` and :attr:`zoom_text`
-    zoom_label : :class:`QtWidgets.QLabel`
+    zoom_label : :class:`QtWidgets.QLabel <PySide.QtGui.QLabel>`
         Label the :attr:`zoom_text` text box
-    zoom_text : :class:`QtWidgets.QLineEdit`
+    zoom_text : :class:`QtWidgets.QLineEdit <PySide.QtGui.QLineEdit>`
         Text box to enter the zoom factor. Zoom will change on ``return key``
     view_canvas : :class:`PDSImageViewCanvas`
         canvas to place the image on

pdsspect/roi.py

@@ -139,7 +139,7 @@ def create_ROI(self, points=None):
 
         Returns
         -------
-        coordinates : :class:`np.ndarray`
+        coordinates : :class:`numpy.ndarray`
             ``m x 2`` array of coordinates.
         """
 
@@ -164,14 +164,14 @@ def contains_arr(self, x_arr, y_arr):
 
         Parameters
         ----------
-        x_arr : :class:`np.ndarray`
+        x_arr : :class:`numpy.ndarray`
             Array of x coodinates
-        y_arr : :class:`np.ndarray`
+        y_arr : :class:`numpy.ndarray`
             Array of y coordinates
 
         Returns
         -------
-        result : :class:`np.ndarray`
+        result : :class:`numpy.ndarray`
             Boolean array where coordinates that are in ROI are True
         """
         # NOTE: we use a version of the ray casting algorithm
@@ -230,12 +230,12 @@ def _get_mask_from_roi(self, roi, mask=None):
         ----------
         roi : :class:`ROIBase`
             The region of interest
-        mask : :class:`np.ndarray`
+        mask : :class:`numpy.ndarray`
             Boolean array of the image
 
         Returns
         -------
-        mask : :class:`np.ndarray`
+        mask : :class:`numpy.ndarray`
             Boolean array of the image with ROI coordinates as ``True``
         """
 
@@ -515,7 +515,7 @@ def stop_ROI(self, data_x, data_y):
 
         Returns
         -------
-        coordinates : :class:`np.ndarray`
+        coordinates : :class:`numpy.ndarray`
             Coordinates of points selected
         """
 

pdsspect/selection.py

@@ -75,7 +75,7 @@ def add_ROI(self, coordinates, color):
 
         Parameters
         ----------
-        coordinates : :class:`np.ndarray` or :obj:`tuple`
+        coordinates : :class:`numpy.ndarray` or :obj:`tuple`
             Either a ``(m x 2)`` array or a tuple of two arrays
 
             If an array, the first column are the x coordinates and the second
@@ -110,33 +110,34 @@ class Selection(QtWidgets.QDialog, PDSSpectImageSetViewBase):
         Parent of the view
     controller : :class:`SelectionController`
         View controller
-    type_label : :class:`QtWidgets.QLabel`
+    type_label : :class:`QtWidgets.QLabel <PySide.QtGui.QLabel>`
         Label for the selection menu
-    selection_menu : :class:`QtWidgets.QComboBox`
+    selection_menu : :class:`QtWidgets.QComboBox <PySide.QtGui.QComboBox>`
         Drop down menu of selection types
-    type_layout : :class:`QtWidgets.QHBoxLayout`
+    type_layout : :class:`QtWidgets.QHBoxLayout <PySide.QtGui.QHBoxLayout>`
         Horizontal box layout for selection
-    color_label : :class:`QtWidgets.QLabel`
+    color_label : :class:`QtWidgets.QLabel <PySide.QtGui.QLabel>`
         Label for the :attr:`color_menu`
-    color_menu : :class:`QtWidgets.QComboBox`
+    color_menu : :class:`QtWidgets.QComboBox <PySide.QtGui.QComboBox>`
         Drop down menu for color selection
-    color_layout : :class:`QtWidgets.QHBoxLayout`
+    color_layout : :class:`QtWidgets.QHBoxLayout <PySide.QtGui.QHBoxLayout>`
         Horizontal box layout for color selection
-    opacity_label : :class:`QtWidgets.QLabel`
+    opacity_label : :class:`QtWidgets.QLabel <PySide.QtGui.QLabel>`
         Label for the :attr:`opacity_slider`
-    opacity_slider : :class:`QtWidgets.QSlider`
+    opacity_slider : :class:`QtWidgets.QSlider <PySide.QtGui.QSlider>`
         Slider to determine opacity for ROIs
-    opacity_layout : :class:`QtWidgets.QHBoxLayout`
+    opacity_layout : :class:`QtWidgets.QHBoxLayout <PySide.QtGui.QHBoxLayout>`
         Horizontal box layout for opacity slider
-    clear_current_color_btn : :class:`QtWidgets.QPushButton`
+    clear_current_color_btn : :class:`QtWidgets.QPushButton
+        <PySide.QtGui.QPushButton>`
         Button to clear all ROIs will the current color
-    clear_all_btn : :class:`QtWidgets.QPushButton`
+    clear_all_btn : :class:`QtWidgets.QPushButton <PySide.QtGui.QPushButton>`
         Button to clear all ROIs
-    export_btn : :class:`QtWidgets.QPushButton`
+    export_btn : :class:`QtWidgets.QPushButton <PySide.QtGui.QPushButton>`
         Export ROIs to ``.npz`` file
-    load_btn : :class:`QtWidgets.QPushButton`
+    load_btn : :class:`QtWidgets.QPushButton <PySide.QtGui.QPushButton>`
         Load ROIs from ``.npz`` file
-    main_layout : :class:`QtWidgets.QVBoxLayout`
+    main_layout : :class:`QtWidgets.QVBoxLayout <PySide.QtGui.QVBoxLayout>`
         Vertical Box layout for main layout
     """
 

pdsspect/transforms.py

@@ -75,19 +75,19 @@ class Transforms(QtWidgets.QDialog, PDSSpectImageSetViewBase):
         The view canvas to apply transformations to
     controller : :class:`TransformsController`
         The view's controller
-    flip_x_label : :class:`QtWidgets.QLabel`
+    flip_x_label : :class:`QtWidgets.QLabel <PySide.QtGui.QLabel>`
         Label for :attr:`flip_x_box`
-    flip_x_box : :class:`QtWidgets.QCheckBox`
+    flip_x_box : :class:`QtWidgets.QCheckBox <PySide.QtGui.QCheckBox>`
         Flip x axis when checked
-    flip_y_label : :class:`QtWidgets.QLabel`
+    flip_y_label : :class:`QtWidgets.QLabel <PySide.QtGui.QLabel>`
         Label for :attr:`flip_y_box`
-    flip_y_box : :class:`QtWidgets.QCheckBox`
+    flip_y_box : :class:`QtWidgets.QCheckBox <PySide.QtGui.QCheckBox>`
         Flip y axis when checked
-    swap_xy_label : :class:`QtWidgets.QLabel`
+    swap_xy_label : :class:`QtWidgets.QLabel <PySide.QtGui.QLabel>`
         Label for :attr:`swap_xy_box`
-    swap_xy_box : :class:`QtWidgets.QCheckBox`
+    swap_xy_box : :class:`QtWidgets.QCheckBox <PySide.QtGui.QCheckBox>`
         Swap x and y axis when checked
-    layout : :class:`QtWidgets.QGridLayout`
+    layout : :class:`QtWidgets.QGridLayout <PySide.QtGui.QGridLayout>`
         Layout for widget
     """
 

pdsspect/warningtimer.py

@@ -101,7 +101,7 @@ class WarningTimerController(object):
     ----------
     model : :class:`WarningTimerModel`
         The Warning Timer Model
-    view : :class:`QtWidgets.QMessageBox`
+    view : :class:`QtWidgets.QMessageBox <PySide.QtGui.QMessageBox>`
         A message box with a :class:`WarningTimerModel` model
     """
 
@@ -128,7 +128,7 @@ class WarningTimer(QtWidgets.QMessageBox):
         The Warning Timer Model
     control : :class:`WarningTimerController`
         The controller
-    timer : :class:`QtCore.QTimer`
+    timer : :class:`QtCore.QTimer <PySide.QtCore.QTimer>`
         The timer
     """