opticallyshallowdeep 1.2.2__tar.gz → 1.2.3.post1__tar.gz

{opticallyshallowdeep-1.2.2/opticallyshallowdeep.egg-info → opticallyshallowdeep-1.2.3.post1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: opticallyshallowdeep
-Version: 1.2.2
+Version: 1.2.3.post1
 Summary: Identify optically shallow and deep waters in satellite imagery
 Author: Yulun Wu
 Author-email: yulunwu8@gmail.com
@@ -9,7 +9,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: geopandas
-Requires-Dist: rasterio
+Requires-Dist: rasterio==1.3.9
 Requires-Dist: tifffile==2023.8.12
 Requires-Dist: netCDF4
 Requires-Dist: pyproj
@@ -18,6 +18,15 @@ Requires-Dist: scipy
 Requires-Dist: matplotlib
 Requires-Dist: imagecodecs
 Requires-Dist: tensorflow
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # Optically-Shallow-Deep 
 
@@ -29,7 +38,9 @@ Supported input includes Level-1C (L1C) SAFE files and ACOLITE-processed L2R net
 
 **Publication:** Richardson, G., Foreman, N., Knudby, A., Wu, Y., & Lin, Y. (2024). Global deep learning model for delineation of optically shallow and optically deep water in Sentinel-2 imagery. *Remote Sensing of Environment*, 311, 114302. <a href="https://doi.org/10.1016/j.rse.2024.114302" target="_blank">https://doi.org/10.1016/j.rse.2024.114302</a>
 
-Originally coded by by Galen Richardson and Anders Knudby, modified and packaged by Yulun Wu
+Originally coded by G. Richardson and A. Knudby, modified and packaged by Y. Wu
+
+Models trained by G. Richardson and N. Foreman
 
  
 ## Installation 
@@ -47,7 +58,7 @@ For mac OS:
 
 ```bash
 conda install -c apple tensorflow-deps
-python -m pip install tensorflow-macos
+python -m pip install tensorflow-macos==2.13.0
 ```
 
 
@@ -104,16 +115,24 @@ osd.run(file_L1C, folder_out, file_L2R=file_L2R)
 The L1C file is always required as it contains a built-in cloud mask. Pixels within 8 pixels of the cloud mask are masked to reduce the impact of clouds. 
 
 
-Output is a 1-band geotiff, with values of prediction probability of optically shallow water (OSW): 100 means most likely OSW, 0 means most likely optically deep water (ODW). Non-water pixels are masked. It is recommended to treat pixels between 0 and 40 as ODW, and pixels between 60 and 100 as OSW (Richardson et al., 2024).
+Output is a 1-band geotiff, with values of prediction probability of optically shallow water (OSW): 100 means most likely OSW, 0 means most likely optically deep water (ODW). Non-water pixels are masked. 
 
 A log file, an intermediate multi-band geotiff, and a preview PNG are also generated in the output folder. They can be deleted after the processing. 
 
 
 **Sample Sentinel-2 scene and output:**
 
-<img src="images/TOA.jpeg"  height="500">
+<img src="https://raw.githubusercontent.com/yulunwu8/Optically-Shallow-Deep/main/images/TOA.jpeg"  height="500">
+
+<img src="https://raw.githubusercontent.com/yulunwu8/Optically-Shallow-Deep/main/images/OSW.jpeg"  height="500">
+
+
+## Tips 
+
+It is recommended to treat pixels with values between 0 and 40 as ODW, and those between 60 and 100 as OSW (Richardson et al., 2024).
+
+Users have reported that averaging results from multiple images acquired on different days can help reduce noise and improve the overall accuracy of classification results.
 
-<img src="images/OSW.jpeg"  height="500">
 
 ## Training, test, and validation data 
 

{opticallyshallowdeep-1.2.2 → opticallyshallowdeep-1.2.3.post1}/README.md

@@ -8,7 +8,9 @@ Supported input includes Level-1C (L1C) SAFE files and ACOLITE-processed L2R net
 
 **Publication:** Richardson, G., Foreman, N., Knudby, A., Wu, Y., & Lin, Y. (2024). Global deep learning model for delineation of optically shallow and optically deep water in Sentinel-2 imagery. *Remote Sensing of Environment*, 311, 114302. <a href="https://doi.org/10.1016/j.rse.2024.114302" target="_blank">https://doi.org/10.1016/j.rse.2024.114302</a>
 
-Originally coded by by Galen Richardson and Anders Knudby, modified and packaged by Yulun Wu
+Originally coded by G. Richardson and A. Knudby, modified and packaged by Y. Wu
+
+Models trained by G. Richardson and N. Foreman
 
  
 ## Installation 
@@ -26,7 +28,7 @@ For mac OS:
 
 ```bash
 conda install -c apple tensorflow-deps
-python -m pip install tensorflow-macos
+python -m pip install tensorflow-macos==2.13.0
 ```
 
 
@@ -83,16 +85,24 @@ osd.run(file_L1C, folder_out, file_L2R=file_L2R)
 The L1C file is always required as it contains a built-in cloud mask. Pixels within 8 pixels of the cloud mask are masked to reduce the impact of clouds. 
 
 
-Output is a 1-band geotiff, with values of prediction probability of optically shallow water (OSW): 100 means most likely OSW, 0 means most likely optically deep water (ODW). Non-water pixels are masked. It is recommended to treat pixels between 0 and 40 as ODW, and pixels between 60 and 100 as OSW (Richardson et al., 2024).
+Output is a 1-band geotiff, with values of prediction probability of optically shallow water (OSW): 100 means most likely OSW, 0 means most likely optically deep water (ODW). Non-water pixels are masked. 
 
 A log file, an intermediate multi-band geotiff, and a preview PNG are also generated in the output folder. They can be deleted after the processing. 
 
 
 **Sample Sentinel-2 scene and output:**
 
-<img src="images/TOA.jpeg"  height="500">
+<img src="https://raw.githubusercontent.com/yulunwu8/Optically-Shallow-Deep/main/images/TOA.jpeg"  height="500">
+
+<img src="https://raw.githubusercontent.com/yulunwu8/Optically-Shallow-Deep/main/images/OSW.jpeg"  height="500">
+
+
+## Tips 
+
+It is recommended to treat pixels with values between 0 and 40 as ODW, and those between 60 and 100 as OSW (Richardson et al., 2024).
+
+Users have reported that averaging results from multiple images acquired on different days can help reduce noise and improve the overall accuracy of classification results.
 
-<img src="images/OSW.jpeg"  height="500">
 
 ## Training, test, and validation data 
 

{opticallyshallowdeep-1.2.2 → opticallyshallowdeep-1.2.3.post1}/opticallyshallowdeep/make_multiband_image.py

@@ -10,7 +10,7 @@ def make_multiband_image(file_in,folder_out):
     basename = os.path.basename(file_in).rstrip(".SAFE")
     
     # output path
-    imageFile = os.path.join(folder_out,basename) + '.tif'
+    imageFile = os.path.join(folder_out, f"{basename}.tif")
     
     if os.path.exists(imageFile):
         print('Multi-band geotiff exists: ' + str(imageFile))

{opticallyshallowdeep-1.2.2 → opticallyshallowdeep-1.2.3.post1}/opticallyshallowdeep/run.py

@@ -70,7 +70,7 @@ def run(file_L1C, folder_out, file_L2R = None, to_log=True):
     if file_L2R is None: 
         
         if_SR = False
-        model = 'models/TOA.h5'
+        model = os.path.join('models', 'TOA.h5')
         model_columns = GTOA_model_columns
         file_in = file_L1C
         
@@ -84,7 +84,7 @@ def run(file_L1C, folder_out, file_L2R = None, to_log=True):
             sys.exit('file_L2R does not exist: ' + str(file_L2R))
         
         if_SR = True
-        model = 'models/SR.h5'
+        model = os.path.join('models', 'SR.h5')
         model_columns = GACOLITE_model_columns
         file_in = file_L2R
         

{opticallyshallowdeep-1.2.2 → opticallyshallowdeep-1.2.3.post1/opticallyshallowdeep.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: opticallyshallowdeep
-Version: 1.2.2
+Version: 1.2.3.post1
 Summary: Identify optically shallow and deep waters in satellite imagery
 Author: Yulun Wu
 Author-email: yulunwu8@gmail.com
@@ -9,7 +9,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: geopandas
-Requires-Dist: rasterio
+Requires-Dist: rasterio==1.3.9
 Requires-Dist: tifffile==2023.8.12
 Requires-Dist: netCDF4
 Requires-Dist: pyproj
@@ -18,6 +18,15 @@ Requires-Dist: scipy
 Requires-Dist: matplotlib
 Requires-Dist: imagecodecs
 Requires-Dist: tensorflow
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # Optically-Shallow-Deep 
 
@@ -29,7 +38,9 @@ Supported input includes Level-1C (L1C) SAFE files and ACOLITE-processed L2R net
 
 **Publication:** Richardson, G., Foreman, N., Knudby, A., Wu, Y., & Lin, Y. (2024). Global deep learning model for delineation of optically shallow and optically deep water in Sentinel-2 imagery. *Remote Sensing of Environment*, 311, 114302. <a href="https://doi.org/10.1016/j.rse.2024.114302" target="_blank">https://doi.org/10.1016/j.rse.2024.114302</a>
 
-Originally coded by by Galen Richardson and Anders Knudby, modified and packaged by Yulun Wu
+Originally coded by G. Richardson and A. Knudby, modified and packaged by Y. Wu
+
+Models trained by G. Richardson and N. Foreman
 
  
 ## Installation 
@@ -47,7 +58,7 @@ For mac OS:
 
 ```bash
 conda install -c apple tensorflow-deps
-python -m pip install tensorflow-macos
+python -m pip install tensorflow-macos==2.13.0
 ```
 
 
@@ -104,16 +115,24 @@ osd.run(file_L1C, folder_out, file_L2R=file_L2R)
 The L1C file is always required as it contains a built-in cloud mask. Pixels within 8 pixels of the cloud mask are masked to reduce the impact of clouds. 
 
 
-Output is a 1-band geotiff, with values of prediction probability of optically shallow water (OSW): 100 means most likely OSW, 0 means most likely optically deep water (ODW). Non-water pixels are masked. It is recommended to treat pixels between 0 and 40 as ODW, and pixels between 60 and 100 as OSW (Richardson et al., 2024).
+Output is a 1-band geotiff, with values of prediction probability of optically shallow water (OSW): 100 means most likely OSW, 0 means most likely optically deep water (ODW). Non-water pixels are masked. 
 
 A log file, an intermediate multi-band geotiff, and a preview PNG are also generated in the output folder. They can be deleted after the processing. 
 
 
 **Sample Sentinel-2 scene and output:**
 
-<img src="images/TOA.jpeg"  height="500">
+<img src="https://raw.githubusercontent.com/yulunwu8/Optically-Shallow-Deep/main/images/TOA.jpeg"  height="500">
+
+<img src="https://raw.githubusercontent.com/yulunwu8/Optically-Shallow-Deep/main/images/OSW.jpeg"  height="500">
+
+
+## Tips 
+
+It is recommended to treat pixels with values between 0 and 40 as ODW, and those between 60 and 100 as OSW (Richardson et al., 2024).
+
+Users have reported that averaging results from multiple images acquired on different days can help reduce noise and improve the overall accuracy of classification results.
 
-<img src="images/OSW.jpeg"  height="500">
 
 ## Training, test, and validation data 
 

{opticallyshallowdeep-1.2.2 → opticallyshallowdeep-1.2.3.post1}/opticallyshallowdeep.egg-info/requires.txt

@@ -1,5 +1,5 @@
 geopandas
-rasterio
+rasterio==1.3.9
 tifffile==2023.8.12
 netCDF4
 pyproj

{opticallyshallowdeep-1.2.2 → opticallyshallowdeep-1.2.3.post1}/setup.py

@@ -5,7 +5,7 @@ with open("readme.md", "r") as fh:
 
 setup(
     name='opticallyshallowdeep',
-    version='1.2.2',
+    version='1.2.3.post1',
     author='Yulun Wu',
     author_email='yulunwu8@gmail.com',
     description='Identify optically shallow and deep waters in satellite imagery',
@@ -18,7 +18,7 @@ setup(
         'Programming Language :: Python :: 3'
     ],
     python_requires='>=3.8',
-    install_requires=['geopandas','rasterio','tifffile==2023.8.12','netCDF4','pyproj',
+    install_requires=['geopandas','rasterio==1.3.9','tifffile==2023.8.12','netCDF4','pyproj',
                       'joblib','scipy','matplotlib','imagecodecs','tensorflow']
 )