Closed carshadi closed 1 year ago
Hi,
It appears I am not able to use the imglyb.to_numpy(rai) method
imglyb.to_numpy(rai)
import imglyb import scyjava scyjava.start_jvm() Views = imglyb.util.Views ArrayImgs = scyjava.jimport("net.imglib2.img.array.ArrayImgs") img = ArrayImgs.floats(32,32,32) print(img.dimensionsAsLongArray()) arr = imglyb.to_numpy(img)
yields
[32, 32, 32] Traceback (most recent call last): File "C:\Users\cameron.arshadi\Desktop\repos\imglyb\examples\wrap_arraylike.py", line 13, in <module> arr = imglyb.to_numpy(img) ^^^^^^^^^^^^^^^^^^^^ File "C:\Users\cameron.arshadi\Miniconda3\envs\imglyb-test\Lib\site-packages\imglyb\__init__.py", line 25, in to_numpy return _ImgLibReferenceGuard(source) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\cameron.arshadi\Miniconda3\envs\imglyb-test\Lib\site-packages\imglyb\imglib_ndarray.py", line 67, in __new__ address = get_address(rai) ^^^^^^^^^^^^^^^^ File "C:\Users\cameron.arshadi\Miniconda3\envs\imglyb-test\Lib\site-packages\imglyb\imglib_ndarray.py", line 50, in get_address access = jpype.JObject(class_name_full, rai).update(None) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\cameron.arshadi\Miniconda3\envs\imglyb-test\Lib\site-packages\jpype\_jobject.py", line 59, in __new__ return _JObjectFactory(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\cameron.arshadi\Miniconda3\envs\imglyb-test\Lib\site-packages\jpype\_jobject.py", line 113, in _JObjectFactory raise TypeError("Invalid type conversion to %s requested." % tp) TypeError: Invalid type conversion to ArrayImg [32x32x32] requested.
I used a fresh conda environment on WIndows 10
conda create -n imglyb-test -c conda-forge python=3.9 imglyb conda activate imglyb-test
Downgrading jpype to 1.4.0 and 1.3.0 did not help
1.4.0
1.3.0
Output of conda list
conda list
# packages in environment at C:\Users\cameron.arshadi\Miniconda3\envs\imglyb-test: # # Name Version Build Channel bzip2 1.0.8 h8ffe710_4 conda-forge ca-certificates 2022.12.7 h5b45459_0 conda-forge imglyb 2.0.1 pyh8a188c0_0 conda-forge intel-openmp 2022.2.1 h57928b3_19741 conda-forge jgo 1.0.4 pyhd8ed1ab_0 conda-forge jpype1 1.3.0 py39h2e07f2f_2 conda-forge libblas 3.9.0 16_win64_mkl conda-forge libcblas 3.9.0 16_win64_mkl conda-forge libffi 3.4.2 h8ffe710_5 conda-forge libhwloc 2.8.0 h039e092_1 conda-forge libiconv 1.17 h8ffe710_0 conda-forge liblapack 3.9.0 16_win64_mkl conda-forge libsqlite 3.40.0 hcfcfb64_0 conda-forge libxml2 2.10.3 hc3477c8_0 conda-forge libzlib 1.2.13 hcfcfb64_4 conda-forge maven 3.8.6 h57928b3_0 conda-forge mkl 2022.1.0 h6a75c08_874 conda-forge numpy 1.23.5 py39hbccbffa_0 conda-forge openjdk 17.0.3 h57928b3_4 conda-forge openssl 3.0.7 hcfcfb64_1 conda-forge packaging 22.0 pyhd8ed1ab_0 conda-forge pip 22.3.1 pyhd8ed1ab_0 conda-forge psutil 5.9.4 py39ha55989b_0 conda-forge pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge python 3.9.15 h4de0772_0_cpython conda-forge python_abi 3.9 3_cp39 conda-forge scyjava 1.8.1 pyhd8ed1ab_0 conda-forge setuptools 65.5.1 pyhd8ed1ab_0 conda-forge symlink-exe-runtime 1.0 hcfcfb64_0 conda-forge tbb 2021.7.0 h91493d7_1 conda-forge tk 8.6.12 h8ffe710_0 conda-forge tzdata 2022g h191b570_0 conda-forge ucrt 10.0.22621.0 h57928b3_0 conda-forge vc 14.3 h3d8a991_9 conda-forge vs2015_runtime 14.32.31332 h1d6e394_9 conda-forge wheel 0.38.4 pyhd8ed1ab_0 conda-forge xz 5.2.6 h8d14728_0 conda-forge
Update: installing from source fixed the issue
Hi,
It appears I am not able to use the
imglyb.to_numpy(rai)
methodyields
I used a fresh conda environment on WIndows 10
Downgrading jpype to
1.4.0
and1.3.0
did not helpOutput of
conda list