implementing starMap refactor

spacetx · Oct 10, 2019 · cd62776 · cd62776
1 parent 58eb7ac
commit cd62776
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Showing 15 changed files with 509 additions and 65 deletions.
diff --git a/notebooks/STARmap.ipynb b/notebooks/STARmap.ipynb
@@ -36,7 +36,7 @@
     "import starfish\n",
     "from starfish import IntensityTable\n",
     "import starfish.data\n",
-    "from starfish.types import Axes\n",
+    "from starfish.types import Axes, TraceBuildingStrategies\n",
     "from starfish.util.plot import (\n",
     "    diagnose_registration, imshow_plane, intensity_histogram\n",
     ")\n",
@@ -136,7 +136,7 @@
    "source": [
     "ch_z_max_projector = starfish.image.Filter.Reduce((Axes.CH, Axes.ZPLANE), func=\"max\")\n",
     "projection = ch_r_max_projector.run(stack)\n",
-    "reference_image = projection.sel({Axes.ROUND: 1})\n",
+    "reference_image = projection.sel({Axes.ROUND: 0})\n",
     "\n",
     "ltt = starfish.image.LearnTransform.Translation(\n",
     "    reference_stack=reference_image,\n",
@@ -302,16 +302,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lsbd = starfish.spots.DetectSpots.LocalSearchBlobDetector(\n",
+    "bd = starfish.spots.FindSpots.BlobDetector(\n",
     "    min_sigma=1,\n",
     "    max_sigma=8,\n",
     "    num_sigma=10,\n",
     "    threshold=np.percentile(np.ravel(stack.xarray.values), 95),\n",
-    "    exclude_border=2,\n",
-    "    anchor_round=0,\n",
-    "    search_radius=10,\n",
-    ")\n",
-    "intensities = lsbd.run(scaled, n_processes=8)"
+    "    exclude_border=2)\n",
+    "\n",
+    "spots = bd.run(scaled)"
    ]
   },
   {
@@ -331,7 +329,21 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "decoded = experiment.codebook.decode_per_round_max(IntensityTable(intensities.fillna(0)))\n",
+    "decoder = starfish.spots.DecodeSpots.PerRoundMaxChannel(\n",
+    "    codebook=experiment.codebook,\n",
+    "    anchor_round=0,\n",
+    "    search_radius=10,\n",
+    "    trace_building_strategy=TraceBuildingStrategies.NEAREST_NEIGHBOR)\n",
+    "\n",
+    "decoded = decoder.run(spots=spots)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "decode_mask = decoded['target'] != 'nan'\n",
     "\n",
     "# %gui qt\n",

diff --git a/notebooks/SeqFISH.ipynb b/notebooks/SeqFISH.ipynb
@@ -28,8 +28,7 @@
     "\n",
     "import starfish\n",
     "import starfish.data\n",
-    "from starfish.spots import DetectSpots\n",
-    "from starfish.types import Axes"
+    "from starfish.types import Axes, TraceBuildingStrategies"
    ]
   },
   {
@@ -196,15 +195,19 @@
    "source": [
     "threshold = 0.5\n",
     "\n",
-    "lsbd = starfish.spots.DetectSpots.LocalSearchBlobDetector(\n",
+    "bd = starfish.spots.FindSpots.BlobDetector(\n",
     "    min_sigma=(1.5, 1.5, 1.5),\n",
     "    max_sigma=(8, 8, 8),\n",
     "    num_sigma=10,\n",
-    "    threshold=threshold,\n",
-    "    search_radius=7\n",
-    ")\n",
-    "intensities = lsbd.run(clipped)\n",
-    "decoded = exp.codebook.decode_per_round_max(intensities.fillna(0))"
+    "    threshold=threshold)\n",
+    "\n",
+    "spots = bd.run(clipped)\n",
+    "decoder = starfish.spots.DecodeSpots.PerRoundMaxChannel(\n",
+    "    codebook=exp.codebook,\n",
+    "    search_radius=7,\n",
+    "    trace_building_strategy=TraceBuildingStrategies.NEAREST_NEIGHBOR)\n",
+    "\n",
+    "decoded = decoder.run(spots=spots)"
    ]
   },
   {
@@ -213,7 +216,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "starfish.display(clipped, intensities)"
+    "starfish.display(clipped, decoded)"
    ]
   },
   {

diff --git a/notebooks/py/STARmap.py b/notebooks/py/STARmap.py
@@ -26,7 +26,7 @@
 import starfish
 from starfish import IntensityTable
 import starfish.data
-from starfish.types import Axes
+from starfish.types import Axes, TraceBuildingStrategies
 from starfish.util.plot import (
     diagnose_registration, imshow_plane, intensity_histogram
 )
@@ -97,7 +97,7 @@
 # EPY: START code
 ch_z_max_projector = starfish.image.Filter.Reduce((Axes.CH, Axes.ZPLANE), func="max")
 projection = ch_r_max_projector.run(stack)
-reference_image = projection.sel({Axes.ROUND: 1})
+reference_image = projection.sel({Axes.ROUND: 0})
 
 ltt = starfish.image.LearnTransform.Translation(
     reference_stack=reference_image,
@@ -213,16 +213,14 @@ def plot_scaling_result(
 # EPY: END markdown
 
 # EPY: START code
-lsbd = starfish.spots.DetectSpots.LocalSearchBlobDetector(
+bd = starfish.spots.FindSpots.BlobDetector(
     min_sigma=1,
     max_sigma=8,
     num_sigma=10,
     threshold=np.percentile(np.ravel(stack.xarray.values), 95),
-    exclude_border=2,
-    anchor_round=0,
-    search_radius=10,
-)
-intensities = lsbd.run(scaled, n_processes=8)
+    exclude_border=2)
+
+spots = bd.run(scaled)
 # EPY: END code
 
 # EPY: START markdown
@@ -234,7 +232,16 @@ def plot_scaling_result(
 # EPY: END markdown
 
 # EPY: START code
-decoded = experiment.codebook.decode_per_round_max(IntensityTable(intensities.fillna(0)))
+decoder = starfish.spots.DecodeSpots.PerRoundMaxChannel(
+    codebook=experiment.codebook,
+    anchor_round=0,
+    search_radius=10,
+    trace_building_strategy=TraceBuildingStrategies.NEAREST_NEIGHBOR)
+
+decoded = decoder.run(spots=spots)
+# EPY: END code
+
+# EPY: START code
 decode_mask = decoded['target'] != 'nan'
 
 # %gui qt

diff --git a/notebooks/py/SeqFISH.py b/notebooks/py/SeqFISH.py
@@ -23,8 +23,7 @@
 
 import starfish
 import starfish.data
-from starfish.spots import DetectSpots
-from starfish.types import Axes
+from starfish.types import Axes, TraceBuildingStrategies
 # EPY: END code
 
 # EPY: START markdown
@@ -117,19 +116,23 @@
 # EPY: START code
 threshold = 0.5
 
-lsbd = starfish.spots.DetectSpots.LocalSearchBlobDetector(
+bd = starfish.spots.FindSpots.BlobDetector(
     min_sigma=(1.5, 1.5, 1.5),
     max_sigma=(8, 8, 8),
     num_sigma=10,
-    threshold=threshold,
-    search_radius=7
-)
-intensities = lsbd.run(clipped)
-decoded = exp.codebook.decode_per_round_max(intensities.fillna(0))
+    threshold=threshold)
+
+spots = bd.run(clipped)
+decoder = starfish.spots.DecodeSpots.PerRoundMaxChannel(
+    codebook=exp.codebook,
+    search_radius=7,
+    trace_building_strategy=TraceBuildingStrategies.NEAREST_NEIGHBOR)
+
+decoded = decoder.run(spots=spots)
 # EPY: END code
 
 # EPY: START code
-starfish.display(clipped, intensities)
+starfish.display(clipped, decoded)
 # EPY: END code
 
 # EPY: START markdown

diff --git a/starfish/core/spots/DecodeSpots/per_round_max_channel_decoder.py b/starfish/core/spots/DecodeSpots/per_round_max_channel_decoder.py
@@ -1,9 +1,11 @@
+from typing import Callable, Optional
+
 from starfish.core.codebook.codebook import Codebook
 from starfish.core.intensity_table.decoded_intensity_table import DecodedIntensityTable
 from starfish.core.intensity_table.intensity_table_coordinates import \
     transfer_physical_coords_to_intensity_table
-from starfish.core.spots.DecodeSpots.trace_builders import build_spot_traces_exact_match
-from starfish.core.types import SpotFindingResults
+from starfish.core.spots.DecodeSpots.trace_builders import TRACE_BUILDERS
+from starfish.core.types import SpotFindingResults, TraceBuildingStrategies
 from ._base import DecodeSpotsAlgorithm
 
 
@@ -20,11 +22,28 @@ class PerRoundMaxChannel(DecodeSpotsAlgorithm):
     ----------
     codebook : Codebook
         Contains codes to decode IntensityTable
-
+    trace_building_strategy: TraceBuildingStrategies
+        Defines the strategy for building spot traces to decode across rounds and chs of spot
+        finding results.
+    search_radius : Optional[int]
+        Only applicable if trace_building_strategy is TraceBuildingStrategies.NEAREST_NEIGHBORS.
+        Number of pixels over which to search for spots in other rounds and channels.
+    anchor_round : Optional[int]
+        Only applicable if trace_building_strategy is TraceBuildingStrategies.NEAREST_NEIGHBORS.
+        The imaging round against which other rounds will be checked for spots in the same
+        approximate pixel location.
     """
 
-    def __init__(self, codebook: Codebook):
+    def __init__(
+            self,
+            codebook: Codebook,
+            trace_building_strategy: TraceBuildingStrategies = TraceBuildingStrategies.EXACT_MATCH,
+            anchor_round: Optional[int]=1,
+            search_radius: Optional[int]=3):
         self.codebook = codebook
+        self.trace_builder: Callable = TRACE_BUILDERS[trace_building_strategy]
+        self.anchor_round = anchor_round
+        self.search_radius = search_radius
 
     def run(self, spots: SpotFindingResults, *args) -> DecodedIntensityTable:
         """Decode spots by selecting the max-valued channel in each sequencing round
@@ -40,6 +59,8 @@ def run(self, spots: SpotFindingResults, *args) -> DecodedIntensityTable:
             IntensityTable decoded and appended with Features.TARGET and Features.QUALITY values.
 
         """
-        intensities = build_spot_traces_exact_match(spots)
+        intensities = self.trace_builder(spot_results=spots,
+                                         anchor_round=self.anchor_round,
+                                         search_radius=self.search_radius)
         transfer_physical_coords_to_intensity_table(intensity_table=intensities, spots=spots)
         return self.codebook.decode_per_round_max(intensities)
diff --git a/starfish/core/spots/DecodeSpots/test/__init__.py b/starfish/core/spots/DecodeSpots/test/__init__.py