some notes on win standalone

.gitignore

@@ -2,6 +2,7 @@
 .mypy_cache/
 __pycache__/
 
+__dll__/
 __material__/
 __runtime__/
 __version__/

nutrimorph.py

@@ -88,7 +88,7 @@ start_time = tm_.time()
 
 # --- Images
 image = io_.imread(data_path)
-assert image.ndim == 3
+assert image.ndim == 3 # TODO: replace assertion with proper exception handling
 image = image[:, 512:, 512:]#562
 img_shape = image.shape
 #

standalone/auto-py-to-exe-w-so.json

+{
+    "command_data":{
+	    "onefile":false,
+		"console":true,
+		"additional_files":{
+		    "addFiles_lbb4d":{
+			    "source":"C:/Users/eric/Documents/code/python-to-exe/nutrimorph/main_prm.py",
+				"destination":"."
+			},
+		    "addFiles_aaa0a":{
+			    "source":"C:/Users/eric/Documents/code/python-to-exe/nutrimorph/libblas.dll",
+				"destination":"."
+			},
+		    "addFiles_aaa0b":{
+			    "source":"C:/Users/eric/Documents/code/python-to-exe/nutrimorph/libgcc_s_seh-1.dll",
+				"destination":"."
+			},
+		    "addFiles_aaa0c":{
+			    "source":"C:/Users/eric/Documents/code/python-to-exe/nutrimorph/libgfortran-5.dll",
+				"destination":"."
+			},
+		    "addFiles_aaa0d":{
+			    "source":"C:/Users/eric/Documents/code/python-to-exe/nutrimorph/liblapack.dll",
+				"destination":"."
+			},
+		    "addFiles_aaa0e":{
+			    "source":"C:/Users/eric/Documents/code/python-to-exe/nutrimorph/libquadmath-0.dll",
+				"destination":"."
+			},
+		    "addFiles_aaa0f":{
+			    "source":"C:/Users/eric/Documents/code/python-to-exe/nutrimorph/libwinpthread-1.dll",
+				"destination":"."
+			},
+			"addFiles_ouqe7j":{
+			    "source":"C:/Users/eric/Documents/code/python-to-exe/nutrimorph/frangi3.so",
+				"destination":"."
+			}
+		}
+	},
+	"id_injectable":{
+	    "file":"C:/Users/eric/Documents/code/python-to-exe/nutrimorph/main.py",
+		"icon":"",
+		"output_location":"C:/Users/eric/Documents/code/python-to-exe/nutrimorph/standalone",
+		"VALUE--upx-dir":"",
+		"VALUE--log-level":"",
+		"VALUE-n":"",
+		"VALUE--add-binary":"",
+		"VALUE-p":"",
+		"COMMASPLIT--hidden-import":"",
+		"VALUE--additional-hooks-dir":"",
+		"VALUE--runtime-hook":"",
+		"COMMASPLIT--exclude-module":"",
+		"VALUE--key":"",
+		"VALUE--debug":"",
+		"VALUE--version-file":"",
+		"VALUE-m":"",
+		"VALUE-r":"",
+		"VALUE--osx-bundle-identifier":"",
+		"VALUE--runtime-tmpdir":"",
+		"extra_command_data":""
+	},
+	"switches":{
+	    "disable_recursion_limit":false,
+		"OPTION-a":false,
+		"OPTION--clean":false,
+		"OPTION-s":false,
+		"OPTION--noupx":false,
+		"OPTION--uac-admin":false,
+		"OPTION--uac-uiaccess":false,
+		"OPTION--win-private-assemblies":false,
+		"OPTION--win-no-prefer-redirects":false,
+		"OPTION--bootloader-ignore-signals":false
+	}
+}

standalone/lin-to-win.txt

+Remove all brick... hierarchy in imports
+Remove hierarchy in c-extension loading in frangi3.py
+Change name nutrimorph.py into main.py
+Change name parameters.py into main_prm.py
+In main.py (re-check necessity periodically as this should not be necessary):
+    > import tifffile
+    Then
+    < assert image.ndim == 3 # TODO: replace assertion with proper exception handling
+    ---
+    > if image.ndim == 4:
+    >     image = image[:,:,:,0]
+    > assert image.ndim == 3, f"Image dimension: {image.ndim}={image.shape}, expected 3"
+
+--- Some random notes (should be obsolete)
+
+/mingw64/bin/CC.exe -fPIC  -std=c++11 -O2  -shared  -o libarmadillo.so CMakeFiles/armadillo.dir/src/wrapper1.cpp.obj CMakeFiles/armadillo.dir/src/wrapper2.cpp.obj /mingw64/lib/libblas.dll.a /mingw64/lib/liblapack.dll.a /mingw64/lib/gcc/x86_64-w64-mingw32/9.2.0/libgfortran.a
+
+https://packages.msys2.org/search
+Install libgfortran
+
+Modified link.txt in C:\Users\eric\Documents\code\python-to-exe to point to the appriopriate version of the libraries (.dll.a, not .a)
+Modified shared:
+/mingw64/bin/CC.exe -fPIC  -std=c++11 -O2  -shared  -o libarmadillo.so CMakeFiles/armadillo.dir/src/wrapper1.cpp.obj CMakeFiles/armadillo.dir/src/wrapper2.cpp.obj /mingw64/lib/libblas.dll.a /mingw64/lib/liblapack.dll.a /mingw64/lib/gcc/x86_64-w64-mingw32/9.2.0/libgfortran.a
+Maybe final
+/mingw64/bin/CC.exe -fPIC  -std=c++11 -O2  -shared  -o libarmadillo.so CMakeFiles/armadillo.dir/src/wrapper1.cpp.obj CMakeFiles/armadillo.dir/src/wrapper2.cpp.obj /mingw64/lib/libblas.dll.a /mingw64/lib/liblapack.dll.a
+
+
+$ cd /mingw64/x86_64-w64-mingw32/include
+$ ln -s /usr/include/armadillo
+$ ln -s /usr/include/armadillo_bits
+
+$ cd /mingw64/lib/
+$ ln -s /usr/lib/libarmadillo.so
+
+
+$ find /c/Users/eric/Documents/code/armadillo/armadillo-9.800.3 -name '*.obj'
+./CMakeFiles/armadillo.dir/src/wrapper1.cpp.obj
+./CMakeFiles/armadillo.dir/src/wrapper2.cpp.obj
+
+If tifffile is missing, then DIO_6H_6_1.70bis_2.2_3.tif, when read with skimage.imread, appears as a 4-D (last dim=color) image which only contains zeros in the first channel.