Rotate image in Imviz

CHANGES.rst

@@ -18,6 +18,9 @@ Cubeviz
 Imviz
 ^^^^^
 
+- New Simple Image Rotation plugin to rotate the celestial axes of
+  images if they have valid WCS. [#1340]
+
 Mosviz
 ^^^^^^
 

docs/imviz/plugins.rst

@@ -251,3 +251,39 @@ The columns are as follow:
 
 Once you have the results in a table, you can further manipulated them as
 documented in :ref:`astropy:astropy-table`.
+
+
+.. _rotate-image-simple:
+
+Simple Image Rotation
+=====================
+
+.. warning::
+
+    Distortion is ignored, so using this plugin on distorted data is
+    not recommended.
+
+.. note::
+
+    Zoom box in :ref:`imviz-compass` will not show when rotation mode is on.
+
+This plugins rotates image(s) by its celestial axes by the given angle.
+You can toggle the rotation mode on and off. You can select viewer and data
+but those options only show when applicable. You can enter the desired
+rotation angle in degrees. When the angle is zero, it will align image(s) to
+N-up and E-left orientation. If an image does not have a valid WCS, it will
+not be rotated. Click on the :guilabel:`ROTATE` button to finalize.
+
+Given that this plugin affects the linking of the entire data collection
+in Imviz by introducing a hidden data layer with the desired WCS,
+it is not recommended to keep toggling this on and off continuously.
+You might also notice some lag when a lot of images are loaded.
+
+Furthermore, linking is global across Imviz, regardless of the viewer.
+Therefore, when WCS is rotated in one viewer, it will propagate to
+the other viewers when multiple viewers are open.
+
+Toggling the rotation mode off would re-orient the viewer to have
+Y-up and X-right for the original reference data but the other data
+would still be linked to it by WCS. To change the linking back to pixels,
+use the :ref:`imviz-link-control` plugin.

docs/reference/api.rst

@@ -126,6 +126,9 @@ Plugins
 .. automodapi:: jdaviz.configs.imviz.plugins.links_control.links_control
    :no-inheritance-diagram:
 
+.. automodapi:: jdaviz.configs.imviz.plugins.rotate_image.rotate_image
+   :no-inheritance-diagram:
+
 .. automodapi:: jdaviz.configs.mosviz.plugins.row_lock.row_lock
    :no-inheritance-diagram:
 

jdaviz/app.py

@@ -1017,12 +1017,19 @@ def _viewer_by_reference(self, reference):
 
         Returns
         -------
-        `~glue_jupyter.bqplot.common.BqplotBaseView`
+        viewer : `~glue_jupyter.bqplot.common.BqplotBaseView`
             The viewer class instance.
         """
         viewer_item = self._viewer_item_by_reference(reference)
 
-        return self._viewer_store[viewer_item['id']]
+        # There is a degeneracy between reference and ID.
+        # Imviz falls back to ID for user-created viewers.
+        if viewer_item is not None:
+            viewer = self._viewer_store[viewer_item['id']]
+        else:  # Maybe it is ID
+            viewer = self._viewer_store[reference]
+
+        return viewer
 
     def _viewer_item_by_reference(self, reference):
         """
@@ -1218,10 +1225,12 @@ def _update_selected_data_items(self, viewer_id, selected_items):
 
             # Make everything visible again in Imviz.
             if self.config == 'imviz':
-                from jdaviz.configs.imviz.helper import layer_is_image_data
+                from jdaviz.configs.imviz.helper import layer_is_image_data, layer_is_hidden
 
                 for lyr in viewer.state.layers:
-                    if layer_is_image_data(lyr.layer):
+                    if layer_is_hidden(lyr.layer):
+                        lyr.visible = False
+                    elif layer_is_image_data(lyr.layer):
                         lyr.visible = True
                 viewer.on_limits_change()  # Trigger compass redraw
 

jdaviz/components/viewer_data_select.vue

@@ -114,7 +114,10 @@ module.exports = {
       return true
     },
     itemIsVisible(item, mosvizExtraItems) {
-      if (this.$props.viewer.config === 'mosviz') {
+      if (item.meta.Plugin === 'Simple Image Rotation') {
+        // hide dummy image with fake WCS from that plugin
+        return false
+      } else if (this.$props.viewer.config === 'mosviz') {
         if (this.$props.viewer.reference === 'spectrum-viewer' && item.type !== '1d spectrum') {
           // filters out table, spectrum 2d, images
           return false

jdaviz/configs/imviz/helper.py

@@ -481,13 +481,19 @@ def layer_is_image_data(layer):
     return isinstance(layer, BaseData) and layer.ndim == 2
 
 
+def layer_is_hidden(layer):
+    # This is fake image with rotated WCS from the plugin.
+    return hasattr(layer, 'meta') and layer.meta.get('Plugin', '') == 'Simple Image Rotation'
+
+
 def get_top_layer_index(viewer):
     """Get index of the top visible image layer in Imviz.
     This is because when blinked, first layer might not be top visible layer.
 
     """
     return [i for i, lyr in enumerate(viewer.layers)
-            if lyr.visible and layer_is_image_data(lyr.layer)][-1]
+            if (lyr.visible and layer_is_image_data(lyr.layer) and
+                not layer_is_hidden(lyr.layer))][-1]
 
 
 def get_reference_image_data(app):

jdaviz/configs/imviz/imviz.yaml

@@ -25,6 +25,7 @@ tray:
   - imviz-compass
   - imviz-line-profile-xy
   - imviz-aper-phot-simple
+  - imviz-rotate-image
   - g-export-plot
 viewer_area:
   - container: col

jdaviz/configs/imviz/plugins/__init__.py

@@ -7,3 +7,4 @@
 from .compass import *  # noqa
 from .aper_phot_simple import *  # noqa
 from .line_profile_xy import *  # noqa
+from .rotate_image import *  # noqa

jdaviz/configs/imviz/plugins/line_profile_xy/line_profile_xy.py

@@ -67,7 +67,14 @@ def vue_draw_plot(self, *args, **kwargs):
             self.reset_results()
             return
 
-        x_min, y_min, x_max, y_max = viewer._get_zoom_limits(data)
+        xy_limits = viewer._get_zoom_limits(data)
+        x_limits = xy_limits[:, 0]
+        y_limits = xy_limits[:, 1]
+        x_min = x_limits.min()
+        x_max = x_limits.max()
+        y_min = y_limits.min()
+        y_max = y_limits.max()
+
         comp = data.get_component(data.main_components[0])
         if comp.units:
             y_label = comp.units
@@ -101,8 +108,9 @@ def vue_draw_plot(self, *args, **kwargs):
         y_min = max(int(y_min), 0)
         y_max = min(int(y_max), ny)
         zoomed_data_x = comp.data[y_min:y_max, x]
-        line_x.scales['y'].min = zoomed_data_x.min() * 0.95
-        line_x.scales['y'].max = zoomed_data_x.max() * 1.05
+        if zoomed_data_x.size > 0:
+            line_x.scales['y'].min = zoomed_data_x.min() * 0.95
+            line_x.scales['y'].max = zoomed_data_x.max() * 1.05
 
         fig_y.title = f'Y={y}'
         fig_y.title_style = {'font-size': '12px'}
@@ -119,8 +127,9 @@ def vue_draw_plot(self, *args, **kwargs):
         x_min = max(int(x_min), 0)
         x_max = min(int(x_max), nx)
         zoomed_data_y = comp.data[y, x_min:x_max]
-        line_y.scales['y'].min = zoomed_data_y.min() * 0.95
-        line_y.scales['y'].max = zoomed_data_y.max() * 1.05
+        if zoomed_data_y.size > 0:
+            line_y.scales['y'].min = zoomed_data_y.min() * 0.95
+            line_y.scales['y'].max = zoomed_data_y.max() * 1.05
 
         self.line_plot_across_x = fig_x
         self.line_plot_across_y = fig_y

jdaviz/configs/imviz/plugins/rotate_image/__init__.py

@@ -0,0 +1 @@
+from .rotate_image import *  # noqa

jdaviz/configs/imviz/plugins/rotate_image/rotate_image.py

@@ -0,0 +1,101 @@
+import numpy as np
+from astropy.nddata import NDData
+from traitlets import Any, Bool, observe
+
+from jdaviz.configs.imviz.helper import link_image_data
+from jdaviz.configs.imviz.plugins.parsers import _nddata_to_glue_data
+from jdaviz.configs.imviz.wcs_utils import generate_rotated_wcs
+from jdaviz.core.events import SnackbarMessage
+from jdaviz.core.registries import tray_registry
+from jdaviz.core.template_mixin import TemplateMixin, ViewerSelectMixin, DatasetSelectMixin
+
+__all__ = ['RotateImageSimple']
+
+
+# TODO: Refactor to use Kyle's CSS rotation?
+# TODO: Maybe we do not need DataSelectMixin.
+@tray_registry('imviz-rotate-image', label="Simple Image Rotation")
+class RotateImageSimple(TemplateMixin, ViewerSelectMixin, DatasetSelectMixin):
+    template_file = __file__, "rotate_image.vue"
+
+    rotate_mode_on = Bool(False).tag(sync=True)
+    angle = Any(0).tag(sync=True)
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._theta = 0  # degrees, clockwise
+
+        # Dummy array to go with the rotated WCS, modified as needed later.
+        ndd = NDData(np.zeros((2, 2), dtype=np.uint8), wcs=generate_rotated_wcs(0),
+                     meta={'Plugin': 'Simple Image Rotation'})
+        for cur_data, cur_label in _nddata_to_glue_data(ndd, '_simple_rotated_wcs_ref'):
+            self._data_ref = cur_data
+            self._data_ref_label = cur_label
+            break  # Just the DATA
+
+    def _update_all_viewers(self):
+        for viewer in self.app._viewer_store.values():
+            viewer.update()  # Force viewer to update.
+
+    @observe('rotate_mode_on')
+    def vue_toggle_on_off(self, *args, **kwargs):
+        # It is hard to keep track what the previous reference data was or
+        # if it is still valid, so just brute force here.
+        if not self.rotate_mode_on:
+            for vid in self.app.get_viewer_ids():
+                # This is silent no-op if it is not in that viewer.
+                try:
+                    self.app.remove_data_from_viewer(vid, self._data_ref_label)
+                except Exception:  # nosec B110
+                    pass
+
+    def vue_rotate_image(self, *args, **kwargs):
+        # We only grab the value here to avoid constantly updating as
+        # user is still entering or updating the value.
+        try:
+            self._theta = float(self.angle)
+        except Exception:
+            return
+
+        w_data = self.dataset.selected_dc_item.coords
+        if w_data is None:  # Nothing to do
+            return
+
+        try:
+            # Adjust the fake WCS to data with desired orientation.
+            w_in = generate_rotated_wcs(self._theta)
+
+            # TODO: How to make this more robust?
+            # Match with selected data.
+            w_shape = self.dataset.selected_dc_item.shape
+            sky0 = w_data.pixel_to_world(0, 0)
+            sky1 = w_data.pixel_to_world(w_shape[1] * 0.5, w_shape[0] * 0.5)
+            avg_cdelt = (abs(sky1.ra.deg - sky0.ra.deg) + abs(sky1.dec.deg - sky0.dec.deg)) * 0.5
+            w_in.wcs.crval = np.array([sky1.ra.deg, sky1.dec.deg])
+            w_in.wcs.cdelt = np.array([-avg_cdelt, avg_cdelt])
+            w_in.wcs.set()
+
+            # Add it into data collection if not already there.
+            if self._data_ref_label not in self.app.data_collection.labels:
+                self.app.add_data(self._data_ref, data_label=self._data_ref_label,
+                                  notify_done=False)
+
+            # Update the WCS.
+            self.app.data_collection[self._data_ref_label].coords = w_in
+
+            # Force link by WCS if not already. Otherwise, no point in rotating WCS.
+            # Default settings is enough since we already said distortions are ignored.
+            link_image_data(self.app, link_type='wcs')
+
+            # Make it a reference.
+            self.app.add_data_to_viewer(self.viewer_selected, self._data_ref_label,
+                                        clear_other_data=False)
+            viewer = self.app.get_viewer(self.viewer_selected)
+            if viewer.state.reference_data.label != self._data_ref_label:
+                viewer.state.reference_data = self.app.data_collection[self._data_ref_label]
+
+            # Force all viewers to update.
+            self._update_all_viewers()
+        except Exception as err:  # pragma: no cover
+            self.hub.broadcast(SnackbarMessage(
+                f"Image rotation failed: {repr(err)}", color='error', sender=self))

jdaviz/configs/imviz/plugins/rotate_image/rotate_image.vue

@@ -0,0 +1,48 @@
+<template>
+  <j-tray-plugin>
+    <v-row>
+      <j-docs-link :link="'https://jdaviz.readthedocs.io/en/'+vdocs+'/'+config+'/plugins.html#simple-image-rotation'">Rotate image N-up/E-left.</j-docs-link>
+    </v-row>
+
+    <v-row>
+      <v-switch
+        label="Enable celestial axes rotation"
+        hint="Toggle rotation mode on or off"
+        v-model="rotate_mode_on"
+        persistent-hint>
+      </v-switch>
+    </v-row>
+
+    <div v-if="rotate_mode_on">
+      <plugin-viewer-select
+        :items="viewer_items"
+        :selected.sync="viewer_selected"
+        label="Viewer"
+        hint="Select viewer."
+      />
+
+      <plugin-dataset-select
+        :items="dataset_items"
+        :selected.sync="dataset_selected"
+        :show_if_single_entry="false"
+        label="Data"
+        hint="Select the data to rotate."
+      />
+
+      <v-row>
+        <v-col>
+          <v-text-field
+            v-model="angle"
+            type="number"
+            label="Angle"
+            hint="Rotation angle of N-axis in degrees clockwise (0 is N-up)"
+          ></v-text-field>
+        </v-col>
+      </v-row>
+
+      <v-row justify="end">
+        <v-btn color="primary" text @click="rotate_image">Rotate</v-btn>
+      </v-row>
+    </div>
+  </j-tray-plugin>
+</template>