deleting Decode and Detect modules in lieu of spot finding refactor

docs/source/_static/data_processing_examples/3d_smFISH.py

@@ -20,7 +20,8 @@
 
 import starfish
 import starfish.data
-from starfish import FieldOfView, IntensityTable
+from starfish import FieldOfView, DecodedIntensityTable
+from starfish.types import TraceBuildingStrategies
 
 # equivalent to %gui qt
 ipython = get_ipython()
@@ -57,12 +58,11 @@
 # local intensity maxima, and spots are matched to the gene they represent by looking them up in a
 # codebook that records which (round, channel) matches which gene target.
 
-tlmpf = starfish.spots.DetectSpots.TrackpyLocalMaxPeakFinder(
+tlmpf = starfish.spots.FindSpots.TrackpyLocalMaxPeakFinder(
     spot_diameter=5,  # must be odd integer
     min_mass=0.02,
     max_size=2,  # this is max radius
     separation=7,
-    noise_size=0.65,  # this is not used because preprocess is False
     preprocess=False,
     percentile=10,  # this is irrelevant when min_mass, spot_diameter, and max_size are set properly
     verbose=True,
@@ -100,6 +100,11 @@ def processing_pipeline(
     print("Loading images...")
     images = enumerate(experiment[fov_name].get_images(FieldOfView.PRIMARY_IMAGES))
 
+    decoder = starfish.spots.DecodeSpots.PerRoundMaxChannel(
+        codebook=codebook,
+        trace_building_strategy=TraceBuildingStrategies.SEQUENTIAL
+    )
+
     for image_number, primary_image in images:
         print(f"Filtering image {image_number}...")
         filter_kwargs = dict(
@@ -113,13 +118,12 @@ def processing_pipeline(
         clip2.run(primary_image, **filter_kwargs)
 
         print("Calling spots...")
-        spot_attributes = tlmpf.run(primary_image)
-        all_intensities.append(spot_attributes)
-
-    spot_attributes = IntensityTable.concatenate_intensity_tables(all_intensities)
+        spots = tlmpf.run(primary_image)
+        print("Decoding spots...")
+        decoded_intensities = decoder.run(spots)
+        all_intensities.append(decoded_intensities)
 
-    print("Decoding spots...")
-    decoded = codebook.decode_per_round_max(spot_attributes)
+    decoded = DecodedIntensityTable.concatenate_intensity_tables(all_intensities)
     decoded = decoded[decoded["total_intensity"] > .025]
 
     return primary_image, decoded

docs/source/api/spots/index.rst

@@ -5,8 +5,8 @@ Spots
 
 Starfish provides a number of methods for which spots (or other regions of interest) are the main substrate.
 These include :py:class:`starfish.spots.DetectPixels`, which exposes methods that identify which target code best corresponds to each pixel, and merges adjacent pixels into ROIs,
-:py:class:`starfish.spots.DetectSpots`, which exposes methods that find bright spots against dark backgrounds,
-:py:class:`starfish.spots.Decode`, which exposes methods that match patterns of spots detected across rounds and channels in the same spatial positions with target codes, and
+:py:class:`starfish.spots.FindSpots`, which exposes methods that find bright spots against dark backgrounds,
+:py:class:`starfish.spots.DecodeSpots`, which exposes methods that match patterns of spots detected across rounds and channels in the same spatial positions with target codes, and
 :py:class:`starfish.spots.AssignTargets`, which exposes methods to assign spots to cells.
 
 .. _detect_pixels:
@@ -23,29 +23,11 @@ Pixel Detectors can be imported using ``starfish.spots.DetectPixels``, which reg
 .. automodule:: starfish.spots.DetectPixels
     :members:
 
-
-.. _detection:
-
-Detecting Spots
----------------
-
-Spot Detectors can be imported using ``starfish.spots.DetectSpots``, which registers all classes that subclass ``DetectSpotsAlgorithm``:
-
-.. code-block:: python
-
-    from starfish.spots import DetectSpots
-
-.. automodule:: starfish.spots.DetectSpots
-    :members:
-
 .. _spot_finding:
 
 Finding Spots
 ---------------
 
-NOTE: Starfish is embarking on a SpotFinding data structures refactor see `Spot Finding Refactor Plan`_
-DetectSpots will be replaced by the FindSpots module documented below.
-
 Spot Finders can be imported using ``starfish.spots.FindSpots``, which registers all classes that subclass ``FindSpotsAlgorithm``:
 
 
@@ -58,21 +40,6 @@ Spot Finders can be imported using ``starfish.spots.FindSpots``, which registers
 .. automodule:: starfish.spots.FindSpots
     :members:
 
-
-.. _decoding:
-
-Decoding
---------
-
-Decoders can be imported using ``starfish.spots.Decode``, which registers all classes that subclass ``DecodeAlgorithm``:
-
-.. code-block:: python
-
-    from starfish.spots import Decode
-
-.. automodule:: starfish.spots.Decode
-   :members:
-
 .. _decode_spots:
 
 Decoding Spots

docs/source/index.rst

@@ -69,8 +69,8 @@ To see what improvements the developers have planned for starfish, please see th
   <h2>Features</h2>
 
 * Filtering: :ref:`API <filtering>`
-* Spot-Finding: :ref:`API <detection>`
-* Decoding: :ref:`API <decoding>`
+* Spot-Finding: :ref:`API <spot_finding>`
+* Decoding: :ref:`API <decode_spots>`
 * Segmenting: :ref:`API <segmentation>`
 
 .. raw:: html

starfish/core/pipeline/algorithmbase.py

@@ -2,7 +2,6 @@
 import inspect
 from abc import ABCMeta
 
-from starfish.core.imagestack.imagestack import ImageStack
 from starfish.core.types._constants import STARFISH_EXTRAS_KEY
 
 
@@ -35,16 +34,12 @@ def helper(*args, **kwargs):
                     spot_results = kwargs['spots']
                     spot_results.log.update_log(args[0])
                     result.attrs[STARFISH_EXTRAS_KEY] = spot_results.log.encode()
-                # OLD CODE FOR DETECT WILL GET REMOVED
-                if 'DetectSpots' in method_class_str or 'DetectPixels' in method_class_str:
-                    if isinstance(args[1], ImageStack):
-                        stack = args[1]
-                        # update log with spot detection instance args[0]
-                        stack.log.update_log(args[0])
-                        # get resulting intensity table and set log
-                        it = result
-                        if isinstance(result, tuple):
-                            it = result[0]
-                        it.attrs[STARFISH_EXTRAS_KEY] = stack.log.encode()
+                if 'DetectPixels' in method_class_str:
+                    stack = args[1]
+                    # update log with spot detection instance args[0]
+                    stack.log.update_log(args[0])
+                    # get resulting intensity table and set log
+                    it = result[0]
+                    it.attrs[STARFISH_EXTRAS_KEY] = stack.log.encode()
             return result
         return helper