[9/5] ENH: replace hidden imports with public ones (#405)

starfish/spots/__init__.py

@@ -1,3 +1,4 @@
+from ._spot_attributes import SpotAttributes
 from ._detector import SpotFinder
 from ._decoder import Decoder
 from ._target_assignment import TargetAssignment

starfish/spots/_detector/_base.py

@@ -3,13 +3,14 @@
 import numpy as np
 import xarray as xr
 
-from starfish.stack import ImageStack
 from starfish.intensity_table import IntensityTable
 from starfish.pipeline.algorithmbase import AlgorithmBase
-from starfish.spots._spot_attributes import SpotAttributes
-from starfish.spots._detector.combine_adjacent_features import ConnectedComponentDecodingResult
+from starfish.spots import SpotAttributes
+from starfish.stack import ImageStack
 from starfish.types import Number
 
+from .combine_adjacent_features import ConnectedComponentDecodingResult
+
 
 class SpotFinderAlgorithmBase(AlgorithmBase):
     def find(

starfish/spots/_detector/detect.py

@@ -7,10 +7,10 @@
 import xarray as xr
 
 from starfish.constants import Indices, Features
-from starfish.stack import ImageStack
 from starfish.intensity_table import IntensityTable
 from starfish.munge import dataframe_to_multiindex
-from starfish.spots._spot_attributes import SpotAttributes
+from starfish.spots import SpotAttributes
+from starfish.stack import ImageStack
 from starfish.types import Number
 
 

starfish/spots/_detector/gaussian.py

@@ -6,16 +6,13 @@
 from skimage.feature import blob_log
 
 from starfish.constants import Features
-from starfish.stack import ImageStack
 from starfish.intensity_table import IntensityTable
-from starfish.spots._spot_attributes import SpotAttributes
-from starfish.spots._detector.detect import (
-    measure_spot_intensity,
-    detect_spots,
-)
+from starfish.spots import SpotAttributes
+from starfish.stack import ImageStack
 from starfish.types import Number
 from starfish.util.argparse import FsExistsType
 from ._base import SpotFinderAlgorithmBase
+from .detect import measure_spot_intensity, detect_spots
 
 
 class GaussianSpotDetector(SpotFinderAlgorithmBase):

starfish/spots/_detector/local_max_peak_finder.py

@@ -4,11 +4,11 @@
 import xarray as xr
 from trackpy import locate
 
-from starfish.stack import ImageStack
 from starfish.intensity_table import IntensityTable
-from starfish.spots._spot_attributes import SpotAttributes
-from starfish.spots._detector.detect import detect_spots
+from starfish.spots import SpotAttributes
+from starfish.stack import ImageStack
 from ._base import SpotFinderAlgorithmBase
+from .detect import detect_spots
 
 
 class LocalMaxPeakFinder(SpotFinderAlgorithmBase):

starfish/spots/_detector/pixel_spot_detector.py

@@ -3,10 +3,10 @@
 from starfish.codebook import Codebook
 from starfish.stack import ImageStack
 from starfish.intensity_table import IntensityTable
-from starfish.spots._detector.combine_adjacent_features import (
+from ._base import SpotFinderAlgorithmBase
+from .combine_adjacent_features import (
     ConnectedComponentDecodingResult, combine_adjacent_features
 )
-from ._base import SpotFinderAlgorithmBase
 
 
 class PixelSpotDetector(SpotFinderAlgorithmBase):

starfish/stack.py

@@ -24,7 +24,7 @@
 from starfish.constants import Coordinates, Indices, Features
 from starfish.errors import DataFormatWarning
 from starfish.intensity_table import IntensityTable
-from starfish.spots._spot_attributes import SpotAttributes
+from starfish.spots import SpotAttributes
 
 _DimensionMetadata = collections.namedtuple("_DimensionMetadata", ['order', 'required'])
 

starfish/starfish.py

@@ -4,12 +4,12 @@
 import cProfile
 from pstats import Stats
 
-from starfish.spots._decoder import Decoder
-from starfish.spots._detector import SpotFinder
-from starfish.image._filter import Filter
-from starfish.spots._target_assignment import TargetAssignment
-from starfish.image._registration import Registration
-from starfish.image._segmentation import Segmentation
+from starfish.spots import Decoder
+from starfish.spots import SpotFinder
+from starfish.image import Filter
+from starfish.spots import TargetAssignment
+from starfish.image import Registration
+from starfish.image import Segmentation
 from .util.argparse import FsExistsType