imviz-round-1.5 (astrowidgets + Glupyter)

README.rst

@@ -25,14 +25,16 @@ repository.
 
 ``jdaviz`` provides data viewers and analysis plugins that can be flexibly
 combined as desired to create interactive applications that fit your workflow.
-Three named preset configurations for common use cases are provided. **Specviz**
-is a tool for visualization and quick-look analysis of 1D astronomical spectra.
-**MOSviz** is a visualization tool for many astronomical spectra,
-typically the output of a multi-object spectrograph (e.g., JWST
-NIRSpec), and includes viewers for 1D and 2D spectra as well as
-contextual information like on-sky views of the spectrograph slit.
-**Cubeviz** provides a view of spectroscopic data cubes (like those to be
-produced by JWST MIRI), along with 1D spectra extracted from the cube.
+Several named preset configurations for common use cases are provided:
+
+* **Specviz**: Visualization and quick-look analysis of 1D astronomical spectra.
+* **MOSviz**: Visualization tool for many astronomical spectra,
+  typically the output of a multi-object spectrograph (e.g., JWST
+  NIRSpec), and includes viewers for 1D and 2D spectra as well as
+  contextual information like on-sky views of the spectrograph slit.
+* **Cubeviz**: View of spectroscopic data cubes (like those to be
+  produced by JWST MIRI), along with 1D spectra extracted from the cube.
+* **Imviz**: Visualization and quick-look analysis of 2D astronomical images.
 
 
 Installing
@@ -41,7 +43,6 @@ For details on installing and using JDAViz, see the
 `Jdaviz documentation <https://jdaviz.readthedocs.io/en/latest/>`_.
 
 
-
 License
 -------
 

docs/imviz/index.rst

@@ -0,0 +1,30 @@
+(TODO: Nice logo here.)
+
+.. _imviz:
+
+#####
+Imviz
+#####
+
+Imviz is a tool for visualization and quick-look analysis of 2D astronomical
+images. Like the rest of `jdaviz`, it is written in the Python programming
+language, and therefore can be run anywhere Python is supported
+(see :doc:`../installation`). Imviz is built on top of the
+`astrowidgets <https://astrowidgets.readthedocs.io>`_ using
+`Glupyter <https://glue-jupyter.readthedocs.io>`_ backend, providing a visual,
+interactive interface to the analysis capabilities in that library.
+
+Imviz allows images to be easily displayed and examined. It supports WCS
+and so on. (TODO: Add content.)
+
+
+Using Imviz
+-----------
+
+To run Imviz in a notebook::
+
+    from jdaviz import Imviz
+    imviz = Imviz()
+    imviz.app
+
+(TODO: Add content.)

docs/index.rst

@@ -38,6 +38,7 @@ Using Jdaviz
   specviz/index.rst
   cubeviz/index.rst
   mosviz/index.rst
+  imviz/index.rst
 
 Reference/API
 =============

docs/quickstart.rst

@@ -40,4 +40,4 @@ or simply start a new Jupyter notebook and run the following in a cell::
     app
 
 To learn more about the various ``jdaviz`` application configurations and loading data, see the :ref:`cubeviz`,
-:ref:`specviz`, or :ref:`mosviz` tools.
+:ref:`specviz`, :ref:`mosviz`, or :ref:`imviz` tools.

jdaviz/__init__.py

@@ -12,3 +12,4 @@
 from jdaviz.configs.specviz2d import Specviz2d  # noqa
 from jdaviz.configs.mosviz import MosViz  # noqa
 from jdaviz.configs.cubeviz import CubeViz  # noqa
+from jdaviz.configs.imviz import Imviz  # noqa

jdaviz/cli.py

@@ -18,8 +18,8 @@
               default='default',
               nargs=1,
               show_default=True,
-              type=click.Choice(['default', 'cubeviz', 'specviz', 'mosviz'],
-                                case_sensitive=False),
+              type=click.Choice(['default', 'cubeviz', 'specviz', 'mosviz',
+                                 'imviz'], case_sensitive=False),
               help="Configuration to use on application startup")
 def main(filename, layout='default'):
     """

jdaviz/configs/__init__.py

@@ -2,3 +2,4 @@
 from .specviz import *  # noqa
 from .default import *  # noqa
 from .mosviz import *  # noqa
+from .imviz import *  # noqa

jdaviz/configs/imviz/__init__.py

@@ -0,0 +1,2 @@
+from .plugins import *  # noqa
+from .helper import Imviz  # noqa

jdaviz/configs/imviz/helper.py

@@ -0,0 +1,12 @@
+from jdaviz.core.helpers import ConfigHelper
+
+__all__ = ['Imviz']
+
+
+class Imviz(ConfigHelper):
+    """Imviz helper class."""
+
+    _default_configuration = "imviz"
+
+    def show(self):
+        self.app

jdaviz/configs/imviz/imviz.ipynb

@@ -0,0 +1,38 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from jdaviz import Imviz\n",
+    "\n",
+    "imviz = Imviz()\n",
+    "imviz.load_data('DATA_FILENAME')\n",
+    "imviz.app"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

jdaviz/configs/imviz/imviz.yaml

@@ -0,0 +1,20 @@
+settings:
+  configuration: imviz
+  data:
+    parser: imviz-image-parser
+  visible:
+    menu_bar: false
+    toolbar: false
+    tray: false
+    tab_headers: false
+  context:
+    notebook:
+      max_height: 600px
+viewer_area:
+  - container: col
+    children:
+      - container: row
+        viewers:
+          - name: Image
+            plot: imviz-image-viewer
+            reference: imviz-image-viewer

jdaviz/configs/imviz/plugins/__init__.py

@@ -0,0 +1,2 @@
+from .viewers import *  # noqa
+from .parsers import *  # noqa

jdaviz/configs/imviz/plugins/parsers.py

@@ -0,0 +1,27 @@
+import pathlib
+
+from astropy.nddata import CCDData
+
+from jdaviz.core.registries import data_parser_registry
+
+__all__ = ["imviz_image_parser"]
+
+
+@data_parser_registry("imviz-image-parser")
+def imviz_image_parser(app, data, data_label=None, show_in_viewer=True):
+    """Loads an image into Imviz"""
+    # If no data label is assigned, give it a unique identifier
+    if not data_label:
+        from astrowidgets.glupyter import _gen_random_label
+        data_label = _gen_random_label(prefix="imviz_data|")
+
+    path = pathlib.Path(data)
+    if path.is_file():
+        # TODO: Support other image formats
+        data = CCDData.read(path)
+    else:
+        raise FileNotFoundError(f"No such file: {path}")
+
+    app.add_data(data, data_label)
+    if show_in_viewer:
+        app.add_data_to_viewer("imviz-image-viewer", data_label, clear_other_data=True)

jdaviz/configs/imviz/plugins/viewers.py

@@ -0,0 +1,68 @@
+from astrowidgets.glupyter import ImageWidget
+from glue.core import BaseData
+
+from jdaviz.core.registries import viewer_registry
+
+__all__ = ['ImvizImageView']
+
+
+@viewer_registry("imviz-image-viewer", label="Image 2D (Imviz)")
+class ImvizImageView(ImageWidget):
+    """Image widget for Imviz."""
+
+    default_class = None
+
+    # session is a glue thing
+    def __init__(self, session, *args, **kwargs):
+
+        super().__init__(*args, **kwargs)
+        self._viewer._session = session
+
+    # More glue things
+
+    def register_to_hub(self, *args, **kwargs):
+        self._viewer.register_to_hub(*args, **kwargs)
+
+    def add_data(self, data):
+        self._viewer.add_data(data)
+        self._link_image_to_cb()
+
+    def remove_data(self, data):
+        self._viewer.remove_data(data)
+        self.viewer.interaction = None
+
+    @property
+    def toolbar_selection_tools(self):
+        return self._viewer.toolbar_selection_tools
+
+    @property
+    def figure_widget(self):
+        return self
+
+    @property
+    def layer_options(self):
+        return self._viewer.layer_options
+
+    @property
+    def viewer_options(self):
+        return self._viewer.viewer_options
+
+    @property
+    def state(self):
+        return self._viewer.state
+
+    def set_plot_axes(self):
+        self.viewer.axes[1].tick_format = None
+        self.viewer.axes[0].tick_format = None
+
+        self.viewer.axes[1].label = "y: pixels"
+        self.viewer.axes[0].label = "x: pixels"
+
+        # Make it so y axis label is not covering tick numbers.
+        self.viewer.axes[1].label_offset = "-50"
+
+    def data(self, cls=None):
+        return [layer_state.layer
+                for layer_state in self._viewer.state.layers
+                if hasattr(layer_state, 'layer') and
+                isinstance(layer_state.layer, BaseData)]

jdaviz/configs/imviz/tests/__init__.py

@@ -0,0 +1 @@
+"""Tests for Imviz image viewer."""

jdaviz/core/config.py

@@ -39,6 +39,8 @@ def read_configuration(path=None):
         path = default_path / "mosviz" / "mosviz.yaml"
     elif path == 'specviz2d':
         path = default_path / "specviz2d" / "specviz2d.yaml"
+    elif path == 'imviz':
+        path = default_path / "imviz" / "imviz.yaml"
     elif not os.path.isfile(path):
         raise ValueError("Configuration must be path to a .yaml file.")