Make IntensityTable and ImageStack mandatory, adjust code to pass lin…

…t & mypy, add docstring

notebooks/test_napari.ipynb

@@ -46,7 +46,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 102/102 [07:40<00:00,  5.67s/it]\n"
+      "100%|██████████| 102/102 [00:03<00:00, 26.80it/s]\n"
      ]
     }
    ],
@@ -58,14 +58,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/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",
+      "/Users/ambrosecarr/projects/spacetx/starfish/.venv/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"
      ]
     }
@@ -84,16 +84,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "102it [00:00, 156.95it/s]\n",
-      "102it [00:00, 131.20it/s]\n",
-      "3it [00:00, 12.05it/s]\n"
+      "102it [00:00, 487.57it/s]\n",
+      "102it [00:00, 576.99it/s]\n",
+      "3it [00:00, 64.72it/s]\n"
      ]
     },
     {
@@ -102,7 +102,7 @@
        "<starfish.ImageStack (r: 1, c: 3, z: 34, y: 2048, x: 2048)>"
       ]
      },
-     "execution_count": 3,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -126,7 +126,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -146,23 +146,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 34/34 [00:00<00:00, 105.84it/s]\n"
+      "100%|██████████| 34/34 [00:00<00:00, 214.03it/s]\n"
      ]
     },
     {
      "data": {
       "text/plain": [
-       "<napari_gui.elements._viewer.Viewer at 0x193d56ba8>"
+       "<napari_gui.elements._viewer.Viewer at 0x1992e52e8>"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -183,24 +193,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 9,
    "metadata": {},
    "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"
+      "100%|██████████| 1/1 [00:00<00:00, 99.96it/s]\n",
+      "100%|██████████| 1/1 [00:00<00:00, 168.60it/s]\n"
      ]
     },
     {
      "data": {
       "text/plain": [
-       "<napari_gui.elements._viewer.Viewer at 0x1916121d0>"
+       "<napari_gui.elements._viewer.Viewer at 0x1931da4e0>"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -210,13 +220,20 @@
     "\n",
     "starfish.plot.show_spots_napari(spots=decoded, background_image=mp)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "starfish",
    "language": "python",
-   "name": "python3"
+   "name": "starfish"
   },
   "language_info": {
    "codemirror_mode": {
@@ -228,7 +245,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.4"
+   "version": "3.6.5"
   }
  },
  "nbformat": 4,

starfish/plot/show_spots_napari.py

@@ -1,38 +1,49 @@
-from numpy import zeros, array
+from numpy import array, zeros
 
-from starfish import IntensityTable
+from starfish import ImageStack, IntensityTable
 from starfish.types import Indices
 
 
 def show_spots_napari(
-	spots: IntensityTable=None,
-	background_image=None,
-	radius_multiplier=30):
-
-	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=coords, face_color='white', edge_color='white',
-						symbol='ring', size=sizes)
-
-	return viewer
+    spots: IntensityTable, background_image: ImageStack, radius_multiplier: int=30
+) -> None:
+    """Display detected spots on a background image using Napari
+
+    Parameters
+    ----------
+    spots : IntensityTable
+        IntensityTable containing spot information. Will be projected to match the coordinates of
+        the background image, if provided.
+    background_image : ImageStack
+        ImageStack containing data to display spots on top of.
+    radius_multiplier : int
+        Multiplies the radius of the displayed spots (default 30)
+    """
+
+    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=coords, face_color='white', edge_color='white', symbol='ring', size=sizes
+    )
+
+    return viewer