fixed napari index

spacetx · Dec 16, 2018 · e5e2b6a · e5e2b6a
1 parent de62eef
commit e5e2b6a
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Showing 2 changed files with 75 additions and 32 deletions.
diff --git a/notebooks/test_napari.ipynb b/notebooks/test_napari.ipynb
@@ -15,7 +15,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib inline\n",
     "%gui qt5\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
@@ -47,7 +46,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 102/102 [00:04<00:00, 21.95it/s]\n"
+      "100%|██████████| 102/102 [07:40<00:00,  5.67s/it]\n"
      ]
     }
    ],
@@ -59,7 +58,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -69,21 +68,10 @@
       "/opt/local/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/vispy/visuals/isocurve.py:22: UserWarning: VisPy is not yet compatible with matplotlib 2.2+\n",
       "  warnings.warn(\"VisPy is not yet compatible with matplotlib 2.2+\")\n"
      ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "(<napari_gui.elements._viewer.Viewer at 0x18513bba8>,\n",
-       " [<Indices.ROUND: 'r'>, <Indices.CH: 'c'>, <Indices.Z: 'z'>])"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
     }
    ],
    "source": [
-    "primary_image.show_stack_napari({})"
+    "viewer, ind = primary_image.show_stack_napari({})"
    ]
   },
   {
@@ -96,16 +84,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "102it [00:00, 202.79it/s]\n",
-      "102it [00:00, 304.91it/s]\n",
-      "3it [00:00, 104.66it/s]\n"
+      "102it [00:00, 156.95it/s]\n",
+      "102it [00:00, 131.20it/s]\n",
+      "3it [00:00, 12.05it/s]\n"
      ]
     },
     {
@@ -114,7 +102,7 @@
        "<starfish.ImageStack (r: 1, c: 3, z: 34, y: 2048, x: 2048)>"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -146,25 +134,35 @@
     "decoded = IntensityTable.load('allen_decoded')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Displaying spots on a 3D image volume\n",
+    "show_spots_napari() projects the provided background image (mirroring language from decoded spots - maybe we should rename) along the rnd and channel axes and overlays the spots as ring markers.\n",
+    "\n",
+    "Spot marker parameters (e.g., opacity, size, color) can be adjusted by double clicking the \"markers\" box in the right panel. They can also be toggled on/off by clicking the \"eye\" checkbox icon."
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 34/34 [00:00<00:00, 106.80it/s]\n"
+      "100%|██████████| 34/34 [00:00<00:00, 105.84it/s]\n"
      ]
     },
     {
      "data": {
       "text/plain": [
-       "<napari_gui.elements._viewer.Viewer at 0x1859f1a20>"
+       "<napari_gui.elements._viewer.Viewer at 0x193d56ba8>"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -175,12 +173,43 @@
     "starfish.plot.show_spots_napari(spots=decoded, background_image=primary_image)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Z projected images\n",
+    "show_spots_napari can also take images projected along the z axis and automatically project the decoded spots along the z axis.\n"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "100%|██████████| 1/1 [00:00<00:00, 56.97it/s]\n",
+      "100%|██████████| 1/1 [00:00<00:00, 128.56it/s]\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<napari_gui.elements._viewer.Viewer at 0x1916121d0>"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "mp = primary_image.max_proj(Indices.CH, Indices.ROUND, Indices.Z)\n",
+    "\n",
+    "starfish.plot.show_spots_napari(spots=decoded, background_image=mp)"
+   ]
   }
  ],
  "metadata": {

diff --git a/starfish/plot/show_spots_napari.py b/starfish/plot/show_spots_napari.py
@@ -1,4 +1,4 @@
-from numpy import array, zeros
+from numpy import zeros, array
 
 from starfish import IntensityTable
 from starfish.types import Indices
@@ -9,16 +9,30 @@ def show_spots_napari(
 	background_image=None,
 	radius_multiplier=30):
 
-	c_r = list(zeros(len(spots.y.values)))
-	coords = array([spots.x.values, spots.y.values, c_r, c_r, spots.z.values]).T
-
 	mp = background_image.max_proj(Indices.CH, Indices.ROUND)
 
+	# Make the array of maker coordinates
+	# If the background image is z projected, also z project the coordinates
+	c_r = zeros(len(spots.y.values))
+	if mp.raw_shape[2] == 1:
+		coords = array([spots.x.values, spots.y.values, c_r, c_r, c_r]).T
+
+	else:
+		coords = array([spots.x.values, spots.y.values, c_r, c_r, spots.z.values]).T
+
+	# Create the Napari viewer with an image stack
 	viewer, axes = mp.show_stack_napari({})
 
+	# This initializes an index for the instantiated marker display
+	# Should be fixed in Napari in the future - KY
+	viewer._index = [0,0,0,0,0]
+
+	# Get the sizes
 	sizes = spots.radius.values * radius_multiplier
 
 	# Add the markers to the viewer
-	viewer.add_markers(coords, face_color='white', edge_color='white', symbol='ring', size=sizes)
+	viewer.add_markers(
+						coords=coords, face_color='white', edge_color='white',
+						symbol='ring', size=sizes)
 
 	return viewer