WIP: deprecate helper-specific methods in specviz/2d

jdaviz/configs/cubeviz/helper.py

@@ -1,3 +1,5 @@
+from astropy.utils.decorators import deprecated
+
 from jdaviz.configs.default.plugins.line_lists.line_list_mixin import LineListMixin
 from jdaviz.configs.specviz import Specviz
 from jdaviz.core.events import AddDataMessage, SnackbarMessage
@@ -112,6 +114,7 @@ def select_wavelength(self, wavelength):
         self.select_slice(wavelength)
 
     @property
+    @deprecated(since="4.2", alternative="viewers['spectrum-viewer']")
     def specviz(self):
         """
         A Specviz helper (:class:`~jdaviz.configs.specviz.helper.Specviz`) for the Jdaviz

jdaviz/configs/default/plugins/data_quality/data_quality.py

@@ -53,8 +53,6 @@ class DataQuality(PluginTemplateMixin, ViewerSelectMixin):
     """
     template_file = __file__, "data_quality.vue"
 
-    irrelevant_msg = Unicode("").tag(sync=True)
-
     # `layer` is the science data layer
     science_layer_multiselect = Bool(False).tag(sync=True)
     science_layer_items = List().tag(sync=True)

jdaviz/configs/default/plugins/model_fitting/model_fitting.py

@@ -79,6 +79,7 @@ class ModelFitting(PluginTemplateMixin, DatasetSelectMixin,
       Label of the residuals to apply when calling :meth:`calculate_fit` if ``residuals_calculate``
       is ``True``.
     * :meth:`calculate_fit`
+    * :meth:`fitted_models`
     """
     dialog = Bool(False).tag(sync=True)
     template_file = __file__, "model_fitting.vue"
@@ -779,6 +780,14 @@ def equation_components(self):
         """
         return re.split(r'[+*/-]', self.equation.value.replace(' ', ''))
 
+    @property
+    def fitted_models(self):
+        """
+        Dictionary of all previously fitted models.
+        """
+        # TODO: store this internally instead of within the app
+        return self.app.fitted_models
+
     def vue_add_model(self, event):
         self.create_model_component()
 

jdaviz/configs/default/plugins/viewers.py

@@ -92,7 +92,7 @@ def user_api(self):
         elif isinstance(self, TableViewer):
             expose += []
         else:
-            expose += ['set_limits', 'reset_limits']
+            expose += ['set_limits', 'reset_limits', 'set_tick_format']
         return ViewerUserApi(self, expose=expose)
 
     @property
@@ -180,6 +180,24 @@ def get_limits(self):
         """
         return self.state.x_min, self.state.x_max, self.state.y_min, self.state.y_max
 
+    def set_tick_format(self, fmt, axis):
+        """
+        Manually set the tick format of one of the axes.
+
+        Parameters
+        ----------
+        fmt : str
+            Format of tick marks.
+            For example, ``'0.1e'`` to set scientific notation or ``'0.2f'`` to turn it off.
+        axis : {x, y}
+            The viewer axis.
+        """
+        if axis not in ('x', 'y'):
+            raise ValueError("axis must be 'x' or 'y'")
+        # Examples of values for fmt are '0.1e' or '0.2f'
+        axis = {'x': 0, 'y': 1}[axis]
+        self.figure.axes[axis].tick_format = fmt
+
     @property
     def native_marks(self):
         """

jdaviz/configs/mosviz/helper.py

@@ -8,6 +8,7 @@
 from astropy import units as u
 from astropy.coordinates import SkyCoord
 from astropy.table import QTable
+from astropy.utils.decorators import deprecated
 from glue.core.data import Data
 from glue.core.exceptions import IncompatibleAttribute
 
@@ -862,6 +863,7 @@ def to_csv(self, filename="MOS_data.csv", selected=False, overwrite=False):
         table_df.to_csv(filename, index_label="Table Index")
 
     @property
+    @deprecated(since="4.2", alternative="viewers['spectrum-viewer']")
     def specviz(self):
         """
         A Specviz helper (:class:`~jdaviz.configs.specviz.helper.Specviz`) for the Jdaviz
@@ -872,6 +874,7 @@ def specviz(self):
         return self._specviz
 
     @property
+    @deprecated(since="4.2", alternative="viewers['spectrum-2d-viewer']")
     def specviz2d(self):
         """
         A Specviz2d helper (:class:`~jdaviz.configs.specviz2d.helper.Specviz2d`) for the Jdaviz

jdaviz/configs/specviz/helper.py

@@ -85,6 +85,7 @@ def load_data(self, data, data_label=None, format=None, show_in_viewer=True,
                           timeout=timeout,
                           load_as_list=load_as_list)
 
+    @deprecated(since="4.2", alternative="get_data")
     def get_spectra(self, data_label=None, spectral_subset=None, apply_slider_redshift="Warn"):
         """Returns the current data loaded into the main viewer
 
@@ -168,6 +169,7 @@ def get_spectral_regions(self, use_display_units=False):
         """
         return self.app.get_subsets(spectral_only=True, use_display_units=use_display_units)
 
+    @deprecated(since="4.2", alternative="viewers['spectrum-viewer'].set_limits")
     def x_limits(self, x_min=None, x_max=None):
         """Sets the limits of the x-axis
 
@@ -190,6 +192,7 @@ def x_limits(self, x_min=None, x_max=None):
         ref_spec = self.get_spectra(ref_index, apply_slider_redshift=False)
         self._set_scale(scale, ref_spec.spectral_axis, x_min, x_max)
 
+    @deprecated(since="4.2", alternative="viewers['spectrum-viewer'].set_limits")
     def y_limits(self, y_min=None, y_max=None):
         """Sets the limits of the y-axis
 
@@ -249,32 +252,37 @@ def _set_scale(self, scale, axis, min_val=None, max_val=None):
 
             scale.max = float(max_val)
 
+    @deprecated(since="4.2", alternative="viewers['spectrum-viewer'].reset_limits")
     def autoscale_x(self):
         """Sets the x-axis limits to the min/max of the reference data
 
         """
         self.x_limits("auto", "auto")
 
+    @deprecated(since="4.2", alternative="viewers['spectrum-viewer'].reset_limits")
     def autoscale_y(self):
         """Sets the y-axis limits to the min/max of the reference data
 
         """
         self.y_limits("auto", "auto")
 
+    @deprecated(since="4.2", alternative="viewers['spectrum-viewer'].set_limits")
     def flip_x(self):
         """Flips the current limits of the x-axis
 
         """
         scale = self.app.get_viewer(self._default_spectrum_viewer_reference_name).scale_x
         self.x_limits(x_min=scale.max, x_max=scale.min)
 
+    @deprecated(since="4.2", alternative="viewers['spectrum-viewer'].set_limits")
     def flip_y(self):
         """Flips the current limits of the y-axis
 
         """
         scale = self.app.get_viewer(self._default_spectrum_viewer_reference_name).scale_y
         self.y_limits(y_min=scale.max, y_max=scale.min)
 
+    @deprecated(since="4.2", alternative="viewers['spectrum-viewer'].set_tick_format")
     def set_spectrum_tick_format(self, fmt, axis=None):
         """
         Manually set the tick format of one of the axes of the profile viewer.
@@ -293,10 +301,7 @@ def set_spectrum_tick_format(self, fmt, axis=None):
             warnings.warn("Please use either 0 or 1 for the axis value")
             return
 
-        # Examples of values for fmt are '0.1e' or '0.2f'
-        self.app.get_viewer(
-            self._default_spectrum_viewer_reference_name
-        ).figure.axes[axis].tick_format = fmt
+        self.viewers[self._default_spectrum_viewer_reference_name].set_tick_format(fmt, axis=['x', 'y'][axis])
 
     def get_data(self, data_label=None, spectral_subset=None, cls=None,
                  use_display_units=False):

jdaviz/configs/specviz2d/helper.py

@@ -1,3 +1,5 @@
+from astropy.utils.decorators import deprecated
+
 from jdaviz.configs.specviz import Specviz
 from jdaviz.core.helpers import ConfigHelper
 from jdaviz.core.events import SnackbarMessage
@@ -19,6 +21,7 @@ def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
     @property
+    @deprecated(since="4.2", alternative="viewers['spectrum-viewer']")
     def specviz(self):
         """
         A Specviz helper (`~jdaviz.configs.specviz.helper.Specviz`) for the Jdaviz
@@ -152,6 +155,7 @@ def load_data(self, spectrum_2d=None, spectrum_1d=None, spectrum_1d_label=None,
                 timeout=timeout
             )
 
+    @deprecated(since="4.2")
     def load_trace(self, trace, data_label, show_in_viewer=True):
         """
         Load a trace object and load into the spectrum-2d-viewer

jdaviz/core/helpers.py

@@ -166,6 +166,7 @@ def viewers(self):
                 for viewer in self.app._viewer_store.values()}
 
     @property
+    @deprecated(since="4.2", alternative="plugins['Model Fitting'].fitted_models")
     def fitted_models(self):
         """
         Returns the fitted models.
@@ -175,9 +176,12 @@ def fitted_models(self):
         parameters : dict
             dict of `astropy.modeling.Model` objects, or None.
         """
+        plg = self.plugins.get('Model Fitting', None)
+        if plg is None:
+            raise ValueError("Model Fitting plugin does not exist")
+        return plg.fitted_models
 
-        return self.app.fitted_models
-
+    @deprecated(since="4.2", alternative="plugins['Model Fitting'].fitted_models")
     def get_models(self, models=None, model_label=None, x=None, y=None):
         """
         Loop through all models and output models of the label model_label.
@@ -239,6 +243,7 @@ def get_models(self, models=None, model_label=None, x=None, y=None):
 
         return selected_models
 
+    @deprecated(since="4.2")
     def get_model_parameters(self, models=None, model_label=None, x=None, y=None):
         """
         Convert each parameter of model inside models into a coordinate that

notebooks/SpecvizExample.ipynb

@@ -124,25 +124,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Or, if you've defined multiple regions, you can retrieve all defined regions/subsets via:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "specviz.get_spectra()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Screenshot Saving"
+    "## Exporting Viewer Image"
    ]
   },
   {
@@ -151,7 +133,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "specviz.app.get_viewer(\"spectrum-viewer\").figure.save_png()"
+    "exp = specviz.plugins['Export']\n",
+    "exp.viewer = 'spectrum-viewer'\n",
+    "exp.export()"
    ]
   },
   {
@@ -160,7 +144,7 @@
    "source": [
     "## Panning/Zooming in Specviz\n",
     "### Limit Methods\n",
-    "You can use the methods x_limits() and y_limits() to modify the field of view of Specviz. You can provide it a scalar (which assumes the units of the loaded spectra), an Astropy Quantity, or 'auto' to automatically scale."
+    "You can use the methods to modify the field of view of the default spectrum viewer. You can provide it a scalar (which assumes the units of the loaded spectra) or an Astropy Quantity."
    ]
   },
   {
@@ -171,9 +155,8 @@
    },
    "outputs": [],
    "source": [
-    "specviz.x_limits()\n",
-    "specviz.x_limits(7*u.um,7.2*u.um)\n",
-    "specviz.y_limits('auto', 170.0)"
+    "specviz.viewers['spectrum-viewer'].get_limits()\n",
+    "specviz.viewers['spectrum-viewer'].set_limits(x_min=7*u.um, x_max=7.2*u.um, y_max=170.0)"
    ]
   },
   {
@@ -190,17 +173,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# axis 1 corresponds to the Y-axis and axis 0 to the X-axis\n",
     "# fmt can be '0.1e' to set scientific notation or '0.2f' to turn it off\n",
-    "specviz.set_spectrum_tick_format(fmt=\"0.2f\", axis=1)"
+    "specviz.viewers['spectrum-viewer'].set_tick_format(fmt=\"0.2f\", axis='x')"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Autoscale Methods\n",
-    "You can also quickly return to the default zoom using autoscale_x() and autoscale_y()"
+    "### Reset Zoom\n",
+    "You can also quickly return to the default zoom"
    ]
   },
   {
@@ -209,8 +191,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "specviz.autoscale_x()\n",
-    "specviz.autoscale_y()"
+    "specviz.viewers['spectrum-viewer'].reset_limits()"
    ]
   },
   {
@@ -227,7 +208,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "specviz.fitted_models"
+    "specviz.plugins['Model Fitting'].fitted_models"
    ]
   },
   {
@@ -243,24 +224,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "specviz.fitted_models['Model']"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Alternatively, the following getter can be used"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "models = specviz.get_models()\n",
-    "models"
+    "specviz.plugins['Model Fitting'].fitted_models['Model']"
    ]
   }
  ],