update incorrect argument and deprecated function for tifffile.TiffWriter

docker/requirements-claratrain.txt

@@ -1,10 +1,10 @@
 openslide-python==1.1.2
-tifffile==2020.9.3
+tifffile>=2022.7.28
 itk==5.1.2
 dask[array,delayed,distributed]==2021.2.0
 dask-cuda==0.17.0
 zarr==2.6.1
 fsspec==0.8.5
 numpy # 1.17.3 already exists in the image
 opencv-contrib-python==4.5.1.48
-imagecodecs==2020.5.30
+imagecodecs>=2021.6.8

docker/requirements-jupyter-dev.txt

@@ -1,13 +1,13 @@
 openslide-python==1.1.2
-tifffile==2020.9.3
+tifffile>=2022.7.28
 itk==5.1.2
 dask[array,delayed,distributed]==2021.2.0
 dask-cuda==0.17.0
 zarr==2.6.1
 fsspec==0.8.5
 numpy==1.19.5
 opencv-contrib-python==4.5.1.48
-imagecodecs==2020.5.30
+imagecodecs>=2021.6.8
 cupy-cuda110==8.4.0
 jupyterlab==3.0.7
 dask_labextension==5.0.0

docker/requirements-jupyter.txt

@@ -1,13 +1,13 @@
 openslide-python==1.1.2
-tifffile==2020.9.3
+tifffile>=2022.7.28
 itk==5.1.2
 dask[array,delayed,distributed]==2021.2.0
 dask-cuda==0.17.0
 zarr==2.6.1
 fsspec==0.8.5
 numpy==1.19.5
 opencv-contrib-python==4.5.1.48
-imagecodecs==2020.5.30
+imagecodecs>=2021.6.8
 cupy-cuda110==8.4.0
 jupyterlab==3.0.7
 dask_labextension==5.0.0

python/cucim/requirements-test.txt

@@ -1,6 +1,7 @@
 GPUtil>=1.4.0
 imagecodecs>=2021.6.8
 openslide-python>=1.1.2
+opencv-python>=4.6
 psutil>=5.8.0
 pytest>=6.2.4
 pytest-cov>=2.12.1

python/cucim/src/cucim/clara/converter/tiff.py

@@ -162,7 +162,7 @@ def svs2tif(input_file, output_folder, tile_size, overlap,
                     else:
                         subfiletype = SUBFILETYPE_NONE
 
-                    tif.save(
+                    tif.write(
                         src_arr,
                         software="Glencoe/Faas pyramid",
                         metadata={"axes": "YXC"},
@@ -174,7 +174,7 @@ def svs2tif(input_file, output_folder, tile_size, overlap,
                             y_resolution // 2 ** level,
                             resolution_unit,
                         ),
-                        compress=("jpeg", 95),  # requires imagecodecs
+                        compression=("jpeg", 95),  # requires imagecodecs
                         subfiletype=subfiletype,
                     )
                 logger.info("Done.")

python/cucim/tests/unit/clara/converter/test_converter.py

@@ -0,0 +1,43 @@
+#
+# Copyright (c) 2022, NVIDIA CORPORATION.
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import os
+from pathlib import Path
+
+
+def test_image_converter_stripe_4096x4096_256_jpeg(
+        tmp_path,
+        testimg_tiff_stripe_4096x4096_256_jpeg):
+    import tifffile
+
+    from cucim.clara.converter import tiff
+
+    tile_size = 128
+    overlap = 0
+    num_workers = os.cpu_count()
+    file_name = "test_image_converter_stripe_4096x4096_256_jpeg-output.tif"
+    output_path = tmp_path / file_name
+    tiff.svs2tif(testimg_tiff_stripe_4096x4096_256_jpeg, Path(tmp_path),
+                 tile_size, overlap, num_workers, file_name)
+    assert os.path.exists(output_path)
+
+    with tifffile.TiffFile(output_path) as tif:
+        assert len(tif.pages) == 6
+        assert tif.pages[0].shape == (4096, 4096, 3)
+        assert tif.pages[0].tile == (128, 128)
+        assert tif.pages[0].compression == tifffile.COMPRESSION.JPEG
+        assert tif.pages[5].shape == (128, 128, 3)
+        assert tif.pages[5].tile == (128, 128)
+        assert tif.pages[5].compression == tifffile.COMPRESSION.JPEG