Merge branch 'master' of https://github.com/clij/clij2-fft

clij · Feb 16, 2024 · be13d33 · be13d33
2 parents 01c695a + f3be702
commit be13d33
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diff --git a/docs/buildlibs/build.md b/docs/buildlibs/build.md
@@ -32,22 +32,32 @@ The c++ library 'clij2fft' implements several FFT based algorithms built on top
 #### Linux/MacOSX Build Instructions
 
 2.  From a bash terminal run [native/cppbuild.sh](https://github.com/clij/clij2-fft/blob/master/native/cppbuild.sh)  
-3.  If step 1 fails check [native/clij2fft/cppbuild.sh](https://github.com/clij/clij2-fft/blob/master/native/clij2fft/cppbuild.sh#L26) and verify that OpenCL and clFFT are installed in the correct locations.
+3.  If step 1 fails check [native/clij2fft/cppbuild.sh](https://github.com/clij/clij2-fft/blob/master/native/clij2fft/cppbuild.sh#L28) and verify that OpenCL and clFFT are installed in the correct locations.
 4.  The updated library (clij2fft.so) and dependencies should now be in the ```clij2-fft/lib/linux64/``` directory.
 
 ### MacOSX and Mac Silicon Native M1
 
-Some users have successfully built the code in a Mac environment. 
-You will need to install `clFFT` from [here](https://formulae.brew.sh/formula/clfft) using [homebrew](https://brew.sh/).
-Note that the `macosx-universal2` binaries were generated using `lipo` (e.g. `lipo -create -output lib/macosx-universal2/libclFFT.dylib lib/macosx/libclFFT.dylib lib/macosx-arm64/libclFFT.dylib`). 
-Currently we recommend searching the [ImageSC Forum](https://forum.image.sc/search?q=apple%20M1%20clij%20deconvolution) for more information.  Please ask questions on the forum if previous discussions are unclear.  
+You will need to install `clFFT` from [here](https://formulae.brew.sh/formula/clfft) using [homebrew](https://brew.sh/).  
 
-We have also found that on macosx the native library libclij2fft needs to be modified with ```install_name_tool``` in order for it to be found by libclij2fft.dylib in it’s current directory (ie when both are in /mambaforge/envs/current_environment/lib)
+To build on macosx or mac m1/m2 (arm64) perform the following
+
+2.  From a bash terminal run [native/cppbuild.sh](https://github.com/clij/clij2-fft/blob/master/native/cppbuild.sh)  
+3.  If step 1 fails check [native/clij2fft/cppbuild.sh](https://github.com/clij/clij2-fft/blob/master/native/clij2fft/cppbuild.sh#L56) and verify that OpenCL and clFFT are installed in the correct locations.
+
+The macosx the native library libclij2fft needs to be modified with ```install_name_tool``` in order for it to be found by libclij2fft.dylib in it’s current directory (ie when both are in /mambaforge/envs/current_environment/lib)
 
 ```
 install_name_tool -change libclFFT.2.dylib @rpath/libclFFT.2.dylib ../../../lib/macosx-arm64/libclij2fft.dylib
 ```
 
+If targeting both macosx and macosx-arm64 we need to build a universal binary using 'lipo'
+
+```
+lipo -create -output lib/macosx-universal2/libclFFT.dylib lib/macosx/libclFFT.dylib lib/macosx-arm64/libclFFT.dylib`
+```
+
+We recommend searching the [ImageSC Forum](https://forum.image.sc/search?q=apple%20M1%20clij%20deconvolution) for more information.  Please ask questions on the forum if previous discussions are unclear.  
+
 ## Build Java Wrapper and Plugin
 
 1.  A 64 bit c++ compiler is needed to create the wrapper.  In windows from Start menu run ‘x64 Native Tools Command Prompt for VS 2019'.  In Linux/MacOsx make sure a 64 bit c++ compiler (ie gcc) is installed. 

diff --git a/python/Test_Installation.ipynb b/python/Test_Installation.ipynb
diff --git a/python/Test_Installation.py b/python/Test_Installation.py
diff --git a/python/clij2fft/pad.py b/python/clij2fft/pad.py
@@ -84,7 +84,8 @@ def pad(img, paddedsize, mode, constant_values=0):
         mode ([type]): one of the np.pad modes
 
     Returns:
-        [nd array]: padded image
+        padded [nd array]: padded image
+        padding [tuple]: tuple containing the padding used
     """
     padding = tuple(map(lambda i,j: ( math.ceil((i-j)/2), math.floor((i-j)/2) ),paddedsize,img.shape))
 

diff --git a/python/clij2fft/test_richardson_lucy.py b/python/clij2fft/test_richardson_lucy.py
diff --git a/python/clij2fft/test_richardson_lucy_nc.py b/python/clij2fft/test_richardson_lucy_nc.py
diff --git a/python/clij2fft/test_sphere.py b/python/clij2fft/test_sphere.py
diff --git a/python/copylibsconda.sh b/python/copylibsconda.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
-# installs in editable mode, copying the native libraries to the location they are needed
-# NOTE this script needs to be customized for your system and environment name
+# this script is used when installing in editable mode, it copies the native libraries to the 
+# location they are needed NOTE this script needs to be customized for your system and environment 
+# name
 
 KERNEL=(`uname -s | tr [A-Z] [a-z]`)
 ARCH=(`uname -m | tr [A-Z] [a-z]`)