changing more old iss blob code

spacetx · Sep 26, 2019 · 89a13f2 · 89a13f2
1 parent fb9b662
commit 89a13f2
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Showing 7 changed files with 30 additions and 22 deletions.
diff --git a/notebooks/ISS.ipynb b/notebooks/ISS.ipynb
@@ -265,8 +265,7 @@
     "\n",
     "dots_max_projector = Filter.Reduce((Axes.ROUND, Axes.ZPLANE), func=\"max\", module=Filter.Reduce.FunctionSource.np)\n",
     "dots_max = dots_max_projector.run(dots)\n",
-    "# locate spots in a reference image\n",
-    "# spots = lp.run(reference_image=dots_max, image_stack=registered_imgs)\n",
+    "\n",
     "spots = bd.run(image_stack=registered_imgs, reference_image=dots_max)\n",
     "\n",
     "decoder = DecodeSpots.PerRoundMaxChannel(codebook=experiment.codebook)\n",

diff --git a/notebooks/py/ISS.py b/notebooks/py/ISS.py
@@ -178,8 +178,7 @@
 
 dots_max_projector = Filter.Reduce((Axes.ROUND, Axes.ZPLANE), func="max", module=Filter.Reduce.FunctionSource.np)
 dots_max = dots_max_projector.run(dots)
-# locate spots in a reference image
-# spots = lp.run(reference_image=dots_max, image_stack=registered_imgs)
+
 spots = bd.run(image_stack=registered_imgs, reference_image=dots_max)
 
 decoder = DecodeSpots.PerRoundMaxChannel(codebook=experiment.codebook)

diff --git a/starfish/core/spots/Decode/test/test_decoding_without_spots.py b/starfish/core/spots/Decode/test/test_decoding_without_spots.py
@@ -11,12 +11,12 @@ def test_per_round_max_spot_decoding_without_spots():
 
     codebook, image_stack, max_intensity = two_spot_sparse_coded_data_factory()
 
-    bd = starfish.spots.DetectSpots.BlobDetector(
+    bd = starfish.spots.FindSpots.BlobDetector(
         min_sigma=1, max_sigma=1, num_sigma=1, threshold=max_intensity + 0.1)
     no_spots = bd.run(image_stack)
 
-    decode = starfish.spots.Decode.PerRoundMaxChannel(codebook)
-    decoded_no_spots: starfish.DecodedIntensityTable = decode.run(no_spots)
+    decode = starfish.spots.DecodeSpots.PerRoundMaxChannel(codebook)
+    decoded_no_spots: starfish.DecodedIntensityTable = decode.run(spots=no_spots)
 
     decoded_spot_table = decoded_no_spots.to_decoded_dataframe()
 

diff --git a/starfish/core/spots/DecodeSpots/per_round_max_channel_decoder.py b/starfish/core/spots/DecodeSpots/per_round_max_channel_decoder.py
@@ -40,6 +40,7 @@ def run(self, spots: SpotFindingResults, *args) -> DecodedIntensityTable:
             IntensityTable decoded and appended with Features.TARGET and Features.QUALITY values.
 
         """
+        # if no spots
         intensities = build_spot_traces_exact_match(spots)
         transfer_physical_coords_to_intensity_table(intensity_table=intensities, spots=spots)
         return self.codebook.decode_per_round_max(intensities)
diff --git a/starfish/core/types/_spot_finding_results.py b/starfish/core/types/_spot_finding_results.py
@@ -30,8 +30,8 @@ def __init__(
         """
         spot_attributes_list = spot_attributes_list or []
         self._results: MutableMapping[Tuple, SpotAttributes] = {
-            indices: spots
-            for indices, spots in spot_attributes_list
+            tuple(indices[i] for i in AXES_ORDER): spots
+            for spots, indices in spot_attributes_list
         }
         self.physical_coord_ranges: Mapping[Hashable, xr.DataArray] = {
             Axes.X.value: imagestack_coords[Coordinates.X.value],

diff --git a/workflows/wdl/iss_published/recipe.py b/workflows/wdl/iss_published/recipe.py
@@ -2,7 +2,7 @@
 from starfish import FieldOfView
 from starfish.image import Filter
 from starfish.image import ApplyTransform, LearnTransform
-from starfish.spots import DetectSpots
+from starfish.spots import DecodeSpots, FindSpots
 from starfish.types import Axes
 
 
@@ -50,17 +50,24 @@ def process_fov(field_num: int, experiment_str: str):
     filt.run(dots, verbose=True, in_place=True)
     filt.run(nuclei, verbose=True, in_place=True)
 
-    print("Detecting")
-    detector = DetectSpots.BlobDetector(
+    print("Finding Spots")
+    bd = FindSpots.BlobDetector(
         min_sigma=1,
         max_sigma=10,
         num_sigma=30,
         threshold=0.01,
         measurement_type='mean',
     )
 
-    intensities = detector.run(filtered_imgs, blobs_image=dots, blobs_axes=(Axes.ROUND, Axes.ZPLANE))
+    dots_max_projector = Filter.Reduce((Axes.ROUND, Axes.ZPLANE), func="max",
+                                       module=Filter.Reduce.FunctionSource.np)
+    dots_max = dots_max_projector.run(dots)
+
+    spots = bd.run(image_stack=filtered_imgs, reference_image=dots_max)
+
+    print("Decoding Spots")
+    decoder = DecodeSpots.PerRoundMaxChannel(codebook=experiment.codebook)
+    decoded = decoder.run(spots=spots)
 
-    decoded = experiment.codebook.decode_per_round_max(intensities)
     df = decoded.to_decoded_dataframe()
     return df
diff --git a/workflows/wdl/iss_spaceTX/recipe.py b/workflows/wdl/iss_spaceTX/recipe.py
@@ -36,21 +36,23 @@ def process_fov(field_num: int, experiment_str: str):
     tmp = dots.sel({Axes.ROUND:0, Axes.CH:0, Axes.ZPLANE:0})
     dots_threshold = np.percentile(np.ravel(tmp.xarray.values), 50)
 
-    # find spots
-    p = starfish.spots.DetectSpots.BlobDetector(
+    bd = starfish.spots.FindSpots.BlobDetector(
         min_sigma=1,
         max_sigma=10,
         num_sigma=30,
         threshold=dots_threshold,
         measurement_type='mean',
     )
 
-    # blobs = dots; define the spots in the dots image, but then find them again in the stack.
-    intensities = p.run(filtered_imgs, blobs_image=dots, blobs_axes=(Axes.ROUND, Axes.ZPLANE))
+    dots_max_projector = starfish.image.Filter.Reduce(
+        (Axes.ROUND, Axes.ZPLANE), func="max",
+        module=starfish.image.Filter.Reduce.FunctionSource.np)
+    dots_max = dots_max_projector.run(dots)
 
-    # decode
-    decoded = experiment.codebook.decode_per_round_max(intensities)
+    spots = bd.run(image_stack=filtered_imgs, reference_image=dots_max)
+
+    decoder = starfish.spots.DecodeSpots.PerRoundMaxChannel(codebook=experiment.codebook)
+    decoded = decoder.run(spots=spots)
 
-    # save results
     df = decoded.to_decoded_dataframe()
-    return df
+    return df