diff --git a/docs/environment_setup.txt b/docs/environment_setup.txt index 0c6226e..6b69fb9 100644 --- a/docs/environment_setup.txt +++ b/docs/environment_setup.txt @@ -1,32 +1,28 @@ SETUP OF ENVIRONMENT -------------------- -Instruction below is for the setup on Win 10 using CUDA v10.1. Setup will be different depending on -operating system. +Instruction below is for the setup on Win 10. Different versions may be used, but the following setup has been tested. +Setup will be different depending on operating system. 1. Update GPU drivers 2. Install visual studio + individual components: a) MSVC v142 - VS 2019 C++ x64/x86 build tools b) Windows 10 SDK (10.0.18362.0) -3. Download CUDA toolkit 10.1 Update 2 +3. Download CUDA (here v11.4) a) install only 'Developer' and 'Runtime' modules -4. Download CuDNN 7.6.5 for CUDA 10.1 - a) unpack to C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\ +4. Download CuDNN v8.2.1.32 for CUDA 11.4 + a) unpack to C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.4\ 5. Add system variables (Control panel > Edit system environment variables): [NAME & PATH] - a) INCLUDE C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\include - b) LIB C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\lib\x64 + a) INCLUDE C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.4\include + b) LIB C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.4\lib\x64 6. Create Python/Anaconda environment - a) Packages: - tensorflow-gpu==2.3.1 - jupyter-tensorboard - nodejs==0.1.1 - npm==0.1.1 - pybind11==2.5.0 - gputools==0.2.9 - stardist - numpy - pandas - pathlib - tifffile - b) on Windows, install PyOpenCL from pre-made binary: - https://www.lfd.uci.edu/~gohlke/pythonlibs/#pyopencl \ No newline at end of file + a) 1. conda create -n stardistenv python=3.9 + 2. conda activate stardistenv + -------OR------- + 1. python -m virtualenv stardistenv + 2. stardistenv\Scripts\activate + + b) Install packages: + pip install tensorflow jupyter-tensorboard nodejs npm pybind11 gputools stardist pandas pathlib tifffile scikit-tensor-py3 pyopencl + !!! on Windows, install PyOpenCL from pre-made binary (https://www.lfd.uci.edu/~gohlke/pythonlibs/#pyopencl): + i.e. above, in pip install-command change pyopencl to path\to\pyopencl.whl \ No newline at end of file diff --git a/docs/requirements.txt b/docs/requirements.txt index 2498e3f..b6b927f 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,11 +1,15 @@ -tensorflow-gpu # ==2.3.1 +tensorflow jupyter-tensorboard -nodejs # ==0.1.1 -npm # ==0.1.1 -pybind11 # ==2.5.0 -gputools # ==0.2.9 +nodejs +npm +pybind11 +gputools stardist pandas pathlib tifffile +scikit-tensor-py3 pyopencl + +# pip install tensorflow jupyter-tensorboard nodejs npm pybind11 gputools stardist pandas pathlib tifffile scikit-tensor-py3 pyopencl +# ON WIN10 REPLACE PYOPENCL WITH path\to\pyopencl.whl \ No newline at end of file diff --git a/predictSD/labelCollect.py b/predictSD/labelCollect.py index 9c44549..09594c8 100644 --- a/predictSD/labelCollect.py +++ b/predictSD/labelCollect.py @@ -140,7 +140,7 @@ def _get_intensities(self, notnull: tuple) -> dict: if self.image.channels is not None: return {f"Intensity Mean_Ch={ch}": self.image.get_channels(ch)[notnull] for ch in np.arange(0, self.image.channels)} - return {"Intensity": self.image.img[notnull]} + return {"Intensity Mean": self.image.img[notnull]} def _test_img_shapes(self) -> None: """Assert that image and label file shapes match.""" diff --git a/readme.md b/readme.md index cc008cc..6e686ae 100644 --- a/readme.md +++ b/readme.md @@ -8,7 +8,7 @@ each label in the segmentation images is marked by a single, unique value. ## Installation PredictSD requires an environment that is capable of running StarDist. For the creation of such environment, see [StarDist's GitHub-page](https://github.com/stardist/stardist/). Required packages are listed in -'predictSD/docs/requirements.txt'. For installation on Win10 using CUDA 10.1, see +'predictSD/docs/requirements.txt'. For installation on Win10 using CUDA 11.4, see 'predictSD/docs/environment_setup.txt'. ## labelCollect.py