Remove instances where we use expand_dynamic_range in notebooks (#1762

) Replace them with Levels. Test plan: `make -j fast`
spacetx · Jan 31, 2020 · 2e61267 · 2e61267
1 parent c915752
commit 2e61267
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Showing 6 changed files with 14 additions and 14 deletions.
diff --git a/notebooks/BaristaSeq.ipynb b/notebooks/BaristaSeq.ipynb
@@ -36,7 +36,7 @@
     "\n",
     "import starfish\n",
     "import starfish.data\n",
-    "from starfish.types import Axes\n",
+    "from starfish.types import Axes, Levels\n",
     "from starfish.util.plot import (\n",
     "    imshow_plane, intensity_histogram, overlay_spot_calls\n",
     ")\n",
@@ -331,7 +331,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sbp = starfish.image.Filter.Clip(p_max=100, expand_dynamic_range=True)\n",
+    "sbp = starfish.image.Filter.Clip(p_max=100, level_method=Levels.SCALE_BY_CHUNK)\n",
     "scaled = sbp.run(background_corrected, n_processes=1, in_place=False)"
    ]
   },
@@ -393,7 +393,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sbp = starfish.image.Filter.Clip(p_max=99.8, expand_dynamic_range=True)\n",
+    "sbp = starfish.image.Filter.Clip(p_max=99.8, level_method=Levels.SCALE_BY_CHUNK)\n",
     "scaled = sbp.run(background_corrected, n_processes=1, in_place=False)\n",
     "\n",
     "f = plot_scaling_result(background_corrected, scaled)"

diff --git a/notebooks/DARTFISH.ipynb b/notebooks/DARTFISH.ipynb
@@ -27,7 +27,7 @@
     "\n",
     "from starfish import display\n",
     "from starfish import data, FieldOfView\n",
-    "from starfish.types import Features, Axes\n",
+    "from starfish.types import Axes, Features, Levels\n",
     "\n",
     "from starfish import IntensityTable\n",
     "\n",
@@ -117,7 +117,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc_filt = Filter.Clip(p_max=100, expand_dynamic_range=True)\n",
+    "sc_filt = Filter.Clip(p_max=100, level_method=Levels.SCALE_BY_CHUNK)\n",
     "norm_imgs = sc_filt.run(imgs)"
    ]
   },

diff --git a/notebooks/SeqFISH.ipynb b/notebooks/SeqFISH.ipynb
@@ -28,7 +28,7 @@
     "\n",
     "import starfish\n",
     "import starfish.data\n",
-    "from starfish.types import Axes, TraceBuildingStrategies"
+    "from starfish.types import Axes, Levels, TraceBuildingStrategies"
    ]
   },
   {
@@ -136,7 +136,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "clip = starfish.image.Filter.Clip(p_max=99.9, expand_dynamic_range=True, is_volume=True)\n",
+    "clip = starfish.image.Filter.Clip(p_max=99.9, is_volume=True, level_method=Levels.SCALE_BY_CHUNK)\n",
     "scaled = clip.run(background_corrected, in_place=False)"
    ]
   },

diff --git a/notebooks/py/BaristaSeq.py b/notebooks/py/BaristaSeq.py
@@ -26,7 +26,7 @@
 
 import starfish
 import starfish.data
-from starfish.types import Axes
+from starfish.types import Axes, Levels
 from starfish.util.plot import (
     imshow_plane, intensity_histogram, overlay_spot_calls
 )
@@ -246,7 +246,7 @@
 # EPY: END markdown
 
 # EPY: START code
-sbp = starfish.image.Filter.Clip(p_max=100, expand_dynamic_range=True)
+sbp = starfish.image.Filter.Clip(p_max=100, level_method=Levels.SCALE_BY_CHUNK)
 scaled = sbp.run(background_corrected, n_processes=1, in_place=False)
 # EPY: END code
 
@@ -292,7 +292,7 @@ def plot_scaling_result(
 # EPY: END markdown
 
 # EPY: START code
-sbp = starfish.image.Filter.Clip(p_max=99.8, expand_dynamic_range=True)
+sbp = starfish.image.Filter.Clip(p_max=99.8, level_method=Levels.SCALE_BY_CHUNK)
 scaled = sbp.run(background_corrected, n_processes=1, in_place=False)
 
 f = plot_scaling_result(background_corrected, scaled)

diff --git a/notebooks/py/DARTFISH.py b/notebooks/py/DARTFISH.py
@@ -22,7 +22,7 @@
 
 from starfish import display
 from starfish import data, FieldOfView
-from starfish.types import Features, Axes
+from starfish.types import Axes, Features, Levels
 
 from starfish import IntensityTable
 
@@ -80,7 +80,7 @@
 # EPY: END markdown
 
 # EPY: START code
-sc_filt = Filter.Clip(p_max=100, expand_dynamic_range=True)
+sc_filt = Filter.Clip(p_max=100, level_method=Levels.SCALE_BY_CHUNK)
 norm_imgs = sc_filt.run(imgs)
 # EPY: END code
 

diff --git a/notebooks/py/SeqFISH.py b/notebooks/py/SeqFISH.py
@@ -23,7 +23,7 @@
 
 import starfish
 import starfish.data
-from starfish.types import Axes, TraceBuildingStrategies
+from starfish.types import Axes, Levels, TraceBuildingStrategies
 # EPY: END code
 
 # EPY: START markdown
@@ -83,7 +83,7 @@
 # EPY: END markdown
 
 # EPY: START code
-clip = starfish.image.Filter.Clip(p_max=99.9, expand_dynamic_range=True, is_volume=True)
+clip = starfish.image.Filter.Clip(p_max=99.9, is_volume=True, level_method=Levels.SCALE_BY_CHUNK)
 scaled = clip.run(background_corrected, in_place=False)
 # EPY: END code