Replace scikit-image with tifffile (#106)

requirements.txt

@@ -5,4 +5,4 @@ packaging
 pathlib;python_version<"3.0"
 numpy
 requests
-scikit-image
+tifffile

slicedimage/_formats.py

@@ -12,11 +12,14 @@ def to_file_obj_or_str(obj):
 
 
 def tiff_reader():
-    # lazy load skimage
-    import skimage.io
+    # lazy load tifffile
+    import tifffile
 
-    return lambda f: skimage.io.imread(to_file_obj_or_str(f))
+    def reader(f):
+        with tifffile.TiffFile(to_file_obj_or_str(f)) as tiff:
+            return tiff.asarray(maxworkers=1)
 
+    return reader
 
 def numpy_reader():
     # lazy load numpy
@@ -30,10 +33,14 @@ def tiff_writer():
     Return a method that accepts (file, array) and saves it to the file.  File may be a file-like
     object, str, or pathlib.Path.
     """
-    # lazy load skimage
-    import skimage.io
+    # lazy load tifffile
+    import tifffile
 
-    return lambda f, arr: skimage.io.imsave(to_file_obj_or_str(f), arr, plugin="tifffile")
+    def writer(f, arr):
+        with tifffile.TiffWriter(to_file_obj_or_str(f)) as tiff:
+            return tiff.save(arr, datetime=None)
+
+    return writer
 
 
 def numpy_writer():

tests/io_/v0_0_0/test_reader.py

@@ -4,8 +4,8 @@
 import tempfile
 import unittest
 
+import tifffile
 import numpy as np
-import skimage.io
 
 import slicedimage
 from slicedimage._dimensions import DimensionNames
@@ -62,7 +62,8 @@ def test_tiff(self):
         with tempfile.TemporaryDirectory() as tempdir:
             # write the tiff file
             data = np.random.randint(0, 65535, size=(120, 80), dtype=np.uint16)
-            skimage.io.imsave(os.path.join(tempdir, "tile.tiff"), data, plugin="tifffile")
+            with tifffile.TiffWriter(os.path.join(tempdir, "tile.tiff")) as tiff:
+                tiff.save(data)
 
             # TODO: (ttung) We should really be producing a tileset programmatically and writing it
             # disk.  However, our current write path only produces numpy output files.

tests/io_/v0_0_0/test_write.py

@@ -5,8 +5,8 @@
 import tempfile
 import unittest
 
+import tifffile
 import numpy as np
-import skimage.io
 
 import slicedimage
 from slicedimage import ImageFormat
@@ -133,7 +133,8 @@ def test_checksum_on_write(self):
         with tempfile.TemporaryDirectory() as tempdir:
             data = np.random.randint(0, 65535, size=(120, 80), dtype=np.uint16)
             file_path = os.path.join(tempdir, "tile.tiff")
-            skimage.io.imsave(file_path, data, plugin="tifffile")
+            with tifffile.TiffWriter(file_path) as tiff:
+                tiff.save(data)
             with open(file_path, "rb") as fh:
                 checksum = hashlib.sha256(fh.read()).hexdigest()
 

tests/io_/v0_1_0/test_reader.py

@@ -4,8 +4,8 @@
 import tempfile
 import unittest
 
+import tifffile
 import numpy as np
-import skimage.io
 
 import slicedimage
 from slicedimage._dimensions import DimensionNames
@@ -62,7 +62,8 @@ def test_tiff(self):
         with tempfile.TemporaryDirectory() as tempdir:
             # write the tiff file
             data = np.random.randint(0, 65535, size=(120, 80), dtype=np.uint16)
-            skimage.io.imsave(os.path.join(tempdir, "tile.tiff"), data, plugin="tifffile")
+            with tifffile.TiffWriter(os.path.join(tempdir, "tile.tiff")) as tiff:
+                tiff.save(data)
 
             # TODO: (ttung) We should really be producing a tileset programmatically and writing it
             # disk.  However, our current write path only produces numpy output files.

tests/io_/v0_1_0/test_write.py

@@ -5,8 +5,8 @@
 import tempfile
 import unittest
 
+import tifffile
 import numpy as np
-import skimage.io
 
 import slicedimage
 from slicedimage import ImageFormat
@@ -133,7 +133,8 @@ def test_checksum_on_write(self):
         with tempfile.TemporaryDirectory() as tempdir:
             data = np.random.randint(0, 65535, size=(120, 80), dtype=np.uint16)
             file_path = os.path.join(tempdir, "tile.tiff")
-            skimage.io.imsave(file_path, data, plugin="tifffile")
+            with tifffile.TiffWriter(file_path) as tiff:
+                tiff.save(data)
             with open(file_path, "rb") as fh:
                 checksum = hashlib.sha256(fh.read()).hexdigest()