Merge pull request #1647 from pllim/all-the-single-pixels

Imviz: Alt-click to create single-pixel region

CHANGES.rst

@@ -40,6 +40,8 @@ Imviz
 
 - Changing link options now updates immediately without needing to press "Link" button. [#1598]
 
+- New tool to create a single-pixel spatial region on the image. [#1647]
+
 Mosviz
 ^^^^^^
 

docs/cubeviz/displaycubes.rst

@@ -100,11 +100,15 @@ Spectrum At Spaxel
 ==================
 
 This tool allows the user to create a one spaxel subset in an image viewer. This subset will then be
-visualized in the spectrum viewer by showing the spectrum at that spaxel. Users can hold down the
-alt key (Alt key on Windows, Option key on Mac) while clicking on a spaxel to create a new subset at
-that point. Users can then compare spectra at different spaxels using the spectrum viewer. Users can
-also utilize the different subset modes that are explained in the
-:ref:`Spatial Regions <imviz_defining_spatial_regions>` section.
+visualized in the spectrum viewer by showing the spectrum at that spaxel.
+Activate this tool and then left-click to create the new region.
+Click again to move the region to a new location under the cursor. Holding down the
+alt key (Alt key on Windows, Option key on Mac) while clicking on a spaxel creates a new subset at
+that point instead of moving the previously created region.
+You can then compare spectra at different spaxels using the spectrum viewer.
+You can also use the subset modes that are explained in the
+:ref:`Spatial Regions <imviz_defining_spatial_regions>`
+section above in the same way you would with the other subset selection tools.
 
 .. _cubeviz-display-settings:
 

docs/imviz/displayimages.rst

@@ -145,6 +145,37 @@ You can :ref:`import <imviz-import-regions-api>` and :ref:`export <imviz_export_
 There are options available in the :guilabel:`Layer` tab under the |icon-settings-sliders| icon
 to make subsets visible or invisible, to change their color, and to change their opacity.
 
+.. _imviz_defining_spatial_regions_single_pixel:
+
+Single-Pixel Selection
+----------------------
+
+This tool allows the user to create a single-pixel spatial region
+in an image viewer. Activate this tool and then left-click to create
+the new region. Click again to move the region to a new location under
+the cursor. Holding down the alt key (Alt key on Windows, Option key
+on Mac) while clicking pixels creates a new region at each point instead
+of moving the previously created region. You can also use the subset
+modes that are explained in the
+:ref:`Spatial Regions <imviz_defining_spatial_regions>`
+section above in the same way you would with the other subset selection
+tools.
+
+When you have multiple images loaded and linked by WCS
+(see :ref:`imviz-link-control`), the region defined is with respect to
+the reference image, which might not be the image you are viewing.
+
+.. warning::
+
+    Region created might not accurately represent area you think you are
+    clicking under the mouse if you click on an image that is zoomed out
+    too much. It is recommended that you zoom in sufficiently to see the
+    individual pixels to use this feature.
+
+.. note::
+
+    Creating too many single-pixel regions may affect performance.
+
 Blinking
 ========
 

jdaviz/configs/cubeviz/plugins/tools.py

@@ -3,12 +3,10 @@
 
 from glue.config import viewer_tool
 from glue.viewers.common.tool import CheckableTool
-from glue.core.roi import RectangularROI
-from glue.core.edit_subset_mode import NewMode
 
 from jdaviz.configs.imviz.plugins.tools import _MatchedZoomMixin
 from jdaviz.core.events import SliceToolStateMessage
-from jdaviz.core.tools import PanZoom
+from jdaviz.core.tools import PanZoom, SinglePixelRegion
 
 __all__ = []
 
@@ -59,49 +57,9 @@ def on_mouse_event(self, data):
 
 
 @viewer_tool
-class SpectrumPerSpaxel(CheckableTool):
+class SpectrumPerSpaxel(SinglePixelRegion):
 
     icon = os.path.join(ICON_DIR, 'pixelspectra.svg')
     tool_id = 'jdaviz:spectrumperspaxel'
     action_text = 'See spectrum at a single spaxel'
     tool_tip = 'Click on the viewer and see the spectrum at that spaxel in the spectrum viewer'
-
-    def __init__(self, viewer, **kwargs):
-        super().__init__(viewer, **kwargs)
-
-    def activate(self):
-        self.viewer.add_event_callback(self.on_mouse_event,
-                                       events=['click'])
-
-    def deactivate(self):
-        self.viewer.remove_event_callback(self.on_mouse_event)
-
-    def on_mouse_event(self, data):
-        event = data['event']
-
-        if event == 'click' and data['altKey'] is True:
-            self.alt_subset_at_spaxel(data)
-        elif event == 'click':
-            self.subset_at_spaxel(data)
-
-    def alt_subset_at_spaxel(self, data):
-        # Add a new subset if the alt key is held down
-        previous_subset_mode = self.viewer.session.edit_subset_mode.mode
-
-        self.viewer.session.edit_subset_mode.mode = NewMode
-        self.subset_at_spaxel(data)
-        self.viewer.session.edit_subset_mode.mode = previous_subset_mode
-
-    def subset_at_spaxel(self, data):
-        x = data['domain']['x']
-        y = data['domain']['y']
-        xmin, xmax, ymin, ymax = self._calc_coords(x, y)
-        self.viewer.apply_roi(RectangularROI(xmin, xmax, ymin, ymax))
-
-    def _calc_coords(self, x, y):
-        xmin = x - 0.5
-        xmax = x + 0.5
-        ymin = y - 0.5
-        ymax = y + 0.5
-
-        return xmin, xmax, ymin, ymax

jdaviz/configs/imviz/plugins/viewers.py

@@ -25,14 +25,15 @@ class ImvizImageView(BqplotImageView, AstrowidgetsImageViewerMixin, JdavizViewer
     tools = ['jdaviz:homezoom', 'jdaviz:boxzoommatch', 'jdaviz:boxzoom',
              'jdaviz:panzoommatch', 'jdaviz:imagepanzoom',
              'jdaviz:contrastbias', 'jdaviz:blinkonce',
-             'bqplot:rectangle', 'bqplot:circle', 'bqplot:ellipse']
+             'bqplot:rectangle', 'bqplot:circle', 'bqplot:ellipse', 'jdaviz:singlepixelregion']
 
     # categories: zoom resets, zoom, pan, subset, select tools, shortcuts
     tools_nested = [
                     ['jdaviz:homezoom', 'jdaviz:prevzoom'],
                     ['jdaviz:boxzoommatch', 'jdaviz:boxzoom'],
                     ['jdaviz:panzoommatch', 'jdaviz:imagepanzoom'],
-                    ['bqplot:circle', 'bqplot:rectangle', 'bqplot:ellipse'],
+                    ['bqplot:circle', 'bqplot:rectangle', 'bqplot:ellipse',
+                     'jdaviz:singlepixelregion'],
                     ['jdaviz:blinkonce', 'jdaviz:contrastbias'],
                     ['jdaviz:sidebar_plot', 'jdaviz:sidebar_export', 'jdaviz:sidebar_compass']
                 ]

jdaviz/configs/imviz/tests/test_tools.py

@@ -1,4 +1,5 @@
 import numpy as np
+from regions import RectanglePixelRegion
 
 from jdaviz.configs.imviz.tests.utils import BaseImviz_WCS_WCS
 
@@ -60,18 +61,53 @@ def test_panzoom_tools(self):
         t_linkedpan.deactivate()
 
 
+# We use a new test class to avoid a dirty state from previous test.
+class TestSinglePixelRegion(BaseImviz_WCS_WCS):
+    def test_singlepixelregion(self):
+        self.imviz.link_data(link_type='wcs')
+
+        t = self.imviz.default_viewer.toolbar_nested.tools['jdaviz:singlepixelregion']
+        t.activate()
+
+        # Create a region while viewing reference data.
+        t.on_mouse_event({'event': 'click', 'altKey': False, 'domain': {'x': 1, 'y': 2}})
+        regions = self.imviz.get_interactive_regions()
+        assert len(regions) == 1
+        reg = regions['Subset 1']
+        assert (isinstance(reg, RectanglePixelRegion) and reg.center.x == 1 and reg.center.y == 2
+                and reg.width == 1 and reg.height == 1)
+
+        # Clicking again will move the region, not creating a new one.
+        t.on_mouse_event({'event': 'click', 'altKey': False, 'domain': {'x': 2, 'y': 3}})
+        regions = self.imviz.get_interactive_regions()
+        assert len(regions) == 1
+        reg = regions['Subset 1']
+        assert (isinstance(reg, RectanglePixelRegion) and reg.center.x == 2 and reg.center.y == 3
+                and reg.width == 1 and reg.height == 1)
+
+        # Create a new region while viewing dithered data.
+        # Region will still be w.r.t. reference data, that is, x and y from domain stay the same.
+        self.imviz.default_viewer.blink_once()
+        t.on_mouse_event({'event': 'click', 'altKey': True, 'domain': {'x': 3, 'y': 4}})
+        regions = self.imviz.get_interactive_regions()
+        assert len(regions) == 2
+        reg = regions['Subset 2']
+        assert (isinstance(reg, RectanglePixelRegion) and reg.center.x == 3 and reg.center.y == 4
+                and reg.width == 1 and reg.height == 1)
+
+        t.deactivate()
+
+
 def test_blink(imviz_helper):
     viewer = imviz_helper.default_viewer
 
     for i in range(3):
         imviz_helper.load_data(np.zeros((2, 2)) + i, data_label=f'image_{i}')
 
-    # Last loaded is shown first. So, blinking will take you back to the first one.
-    # Blink forward. The event will also initialize viewer.label_mouseover .
     viewer.on_mouse_or_key_event({'event': 'keydown', 'key': 'b', 'domain': {'x': 0, 'y': 0}})
     assert viewer.label_mouseover.value == '+0.00000e+00 '
 
-    # Blink forward again and update coordinates info panel.
+    # Blink forward and update coordinates info panel.
     viewer.blink_once()
     viewer.on_mouse_or_key_event({'event': 'mousemove', 'domain': {'x': 0, 'y': 0}})
     assert viewer.label_mouseover.value == '+1.00000e+00 '

jdaviz/core/tools.py

@@ -1,7 +1,7 @@
-import numpy as np
 import os
-from echo import delay_callback
 
+import numpy as np
+from echo import delay_callback
 from glue.config import viewer_tool
 from glue.core import HubListener
 from glue.viewers.common.tool import Tool
@@ -249,3 +249,44 @@ class SidebarShortcutCompass(_BaseSidebarShortcut):
     tool_id = 'jdaviz:sidebar_compass'
     action_text = 'Compass'
     tool_tip = 'Open compass plugin in sidebar'
+
+
+@viewer_tool
+class SinglePixelRegion(CheckableTool):
+
+    icon = os.path.join(ICON_DIR, 'select_single_pixel.svg')
+    tool_id = 'jdaviz:singlepixelregion'
+    action_text = 'Create single-pixel spatial region'
+    tool_tip = 'Define a single-pixel spatial region of interest'
+
+    def activate(self):
+        self.viewer.add_event_callback(self.on_mouse_event, events=['click'])
+
+    def deactivate(self):
+        self.viewer.remove_event_callback(self.on_mouse_event)
+
+    def on_mouse_event(self, data):
+        # Extract data coordinates - these are pixels in the reference image.
+        # NOTE: We always use the reference image pixel coordinates because
+        # Subset is defined w.r.t. reference image.
+        x = data['domain']['x']
+        y = data['domain']['y']
+
+        if data['altKey'] is True:
+            reg = self.get_subset(x, y, as_roi=False)
+            self.viewer.jdaviz_helper.load_regions(reg)
+        else:
+            roi = self.get_subset(x, y, as_roi=True)
+            self.viewer.apply_roi(roi)
+
+    def get_subset(self, x, y, as_roi=False):
+        from regions import RectanglePixelRegion, PixCoord
+        x, y = np.rint([x, y])  # Center on nearest pixel
+        reg = RectanglePixelRegion(center=PixCoord(x=x, y=y), width=1, height=1)
+
+        if as_roi:
+            from jdaviz.core.region_translators import regions2roi
+            roi = regions2roi(reg)
+            return roi
+
+        return reg