profile
viewpoint

odinsbane/least-squares-in-java 20

Java Least Squares fitting library.

odinsbane/tga_reader 3

TGA reader for c++ and java.

odinsbane/jfilament 2

Active countour based segmentation. FIJI plugin.

odinsbane/learning-dominoes 1

A basic dominoes game for practicing machine learning.

odinsbane/pdfr 1

Minimal document organization for keeping track of weekly journal scan reading.

odinsbane/speckletrackerj 1

Automatically exported from code.google.com/p/speckletrackerj

odinsbane/fastshadows 0

This is a small example of using fast shadows to generate shadows. It will be built on GLFW3.

odinsbane/GenericPCA 0

A small library for performing PCA on arbitrary data.

odinsbane/git_n_click 0

A short introduction to using git, along with some example code that uses the python library click.

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha 9006a01c32c68bdff6d494b31d59dccf87e48d0c

Refactored ConnectedComponents2D to use an int[] backing instead of relying on the image pixel type. Did not add performance increase, but prevents the number of labels from exceeding the image pixel value.

view details

push time in 5 days

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha 9546e4e5414a20a7bbe845317d91045ab68f9a75

Only calculates centroids if request. Should be a minor performance improvement.

view details

push time in 5 days

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha 55d6b593025a90a6d01ed7b087afddcc297c0673

Refactoring connected components2d. Made it so getCentroids doesn't have to be called.

view details

push time in 5 days

push eventodinsbane/JLinkExamples

msmith

commit sha 9edc3437998b606973ba765c16aa3363acc82f60

Forgot to repaint the imagepanel.

view details

push time in 13 days

push eventodinsbane/JLinkExamples

msmith

commit sha 7c1dfe531bf41eb33a3a11ccf27da8a1749d563b

IO exceptions appear to be common. Now it waits and tries again.

view details

push time in 13 days

push eventodinsbane/JLinkExamples

msmith

commit sha e7041c584e15e4482c13c89ebc5609a0de69ccae

Added an image viewing widget.

view details

push time in 13 days

push eventodinsbane/jfilament

m smith

commit sha 253d276d853378ee5e10ea7b05512feffc59cf7a

Improving the interface, and fixing the balloon engery.

view details

push time in 15 days

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 582f44b217db3a5fb4c8c2a5172c559e2cd710ff

Refactoring. Working on improving auto mesh detection.

view details

push time in 15 days

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha 638b8cecd5ac43ba1b6e3a028dd181365eb0644a

Made the furrow3d interceptable, added a remove external energy and working on the growing droplet simulation.

view details

msmith

commit sha 3628be7e65a02bfb05358f088a45e9813b86f001

Merge branch 'development' of https://github.com/PaluchLabUCL/DeformingMesh3D-plugin into development

view details

push time in 16 days

push eventodinsbane/jfilament

msmith

commit sha ecfcfb02724307c1cef11cd421bbea5c520bacec

Sometimes broken snakes get in the transform.

view details

push time in 16 days

push eventodinsbane/jfilament

msmith

commit sha 934cea30d67004f4f725105029e6dc8fbf85c29e

Removed the anotation energies.

view details

msmith

commit sha d58b49a2dbe73f9e0de06e43c4fcc8244ec2814f

Improved the exception handling. Now the only handled exceptions are when there are too many points or not enough points. Hopefully will prevent the swallowing of index out of bound exceptions. on that note, fixed an index out of bounds exception on distance transform calculations.

view details

push time in 16 days

push eventodinsbane/jfilament

msmith

commit sha 60bb783735ace11ec0a71e1fa4f29ed222335f97

Intellij broke the line endings. Not a happy day.

view details

push time in 16 days

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha af2c54d63fb0355fca52d5d7ecf87c6c4369591d

Moved the 3d connected components to a package. Working on 'guessing' 3d object.

view details

push time in 16 days

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha be38740de2482e2909466c1605bbc6bde6dedc58

Added an array method to update the line data object. Considering removing the backing array altogether.

view details

push time in 20 days

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha 87a731406ddf4c5d116c5eed5f399b8c69141f5a

fixed the line data object to re-use line array.

view details

push time in 22 days

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 34f268f6f1f35aa596102226e792cfe976dbb89e

Working swap, setup up some line geometries. Need to optimize.

view details

push time in 23 days

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 2ff3182f8b91c2ad0e40051451abc3eaa86f6095

Created a new steric energy that works much better. For the simulations there is also a mean for that helps stabilize things. Transitional, while a new deformation class is put together.

view details

m smith

commit sha 59acbe8db45e7b72c21c02f930c9e710997bbef7

Merge branch 'development' of https://github.com/PaluchLabUCL/DeformingMesh3D-plugin into development

view details

push time in a month

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha 244face1e139f3c955635f799f2e7e97246e3446

Removed the remesh in the filling binary algorithm.

view details

push time in a month

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha dd67b8729d7cf44508dbb0649eec3f3f0ef36e91

working changes. BUG FIX: color suggestions created an infinite loop.

view details

push time in a month

issue commenttensorflow/tensorflow

Unable to build r1.15 using gcc 4.8.5-39 because of -std=c++14 argument.

@Saduf2019 it pretty much says that tensorflow 1.15 is not compatible with gcc 4.8.5. I think the docs should be updated to reflect that. The tested page, https://www.tensorflow.org/install/source#tested_build_configurations that you referenced, should have a tested tf 1.15 and say the accepted gcc to use.

Centos7 still uses 4.8.5 by default, and it would be good to know either stick with tf 1.14 or upgrade gcc for tf 1.15. I'm surprised tf 1.15 should change the gcc requirement, since it appears to be a legacy version.

On Tue, Feb 25, 2020 at 10:21 AM Saduf2019 notifications@github.com wrote:

@odinsbane https://github.com/odinsbane please let us know if above comment helps

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/tensorflow/tensorflow/issues/36892?email_source=notifications&email_token=AA2NNEPZQRYUGVWZ7TZGW2DRETWJ3A5CNFSM4KXX3I4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEM3MVBI#issuecomment-590793349, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA2NNEP6GWXDTCOFFXTCC2TRETWJ3ANCNFSM4KXX3I4A .

odinsbane

comment created time in a month

issue commentspyder-ide/spyder

Spyder doesn't start - no module named 'PyQt5.QtWebEngineWidgets'

Is the issue related to this: https://stackoverflow.com/questions/37876987/cannot-import-qtwebkitwidgets-in-pyqt5 which would mean the version of pyqt5 getting installed is too new?

It seems like everytime I try to use spyder from a conda environment I get this error and I have to recreate the environment and install a specific version for spyder to work.

reisarthur

comment created time in a month

issue commenttensorflow/tensorflow

Unable to build r1.15 using gcc 4.8.5-39 because of -std=c++14 argument.

It looks like mlir was made to require c++14 which is not compatible with gcc 4.8.

https://github.com/tensorflow/tensorflow/commits/r1.15/third_party/mlir/CMakeLists.txt

It sounds like there is a way to disable mlir, but I do not understand how.

odinsbane

comment created time in a month

issue commenttensorflow/tensorflow

Unable to build r1.15 using gcc 4.8.5-39 because of -std=c++14 argument.

It makes it through over 20K jobs before failing. You can see from the log that it is using the -std=c++14, which is not supported in gcc 4.8.

Also, the reference you have provided doesn't say anything about tensorflow 1.15

build-log.txt

odinsbane

comment created time in a month

issue commenttensorflow/tensorflow

Unable to build r1.15 using gcc 4.8.5-39 because of -std=c++14 argument.

PART 2: After modifying the WORKSPACE to include the following:

  # Download the rules_docker repository at release v0.14.1
  http_archive(
      name = "io_bazel_rules_docker",
      sha256 = "dc97fccceacd4c6be14e800b2a00693d5e8d07f69ee187babfd04a80a9f8e250",
      strip_prefix = "rules_docker-0.14.1",
      urls = ["https://github.com/bazelbuild/rules_docker/releases/download/v0.14.1/rules_docker-v0.14.1.tar.gz"],
 )

Then the building gets started:

 vi WORKSPACE 
 bazel build --config=opt --config=cuda //tensorflow/tools/pip_package:build_pip_package
odinsbane

comment created time in a month

issue commenttensorflow/tensorflow

Unable to build r1.15 using gcc 4.8.5-39 because of -std=c++14 argument.

I have included all of the steps, but Ill include all of the log output too. PART 1

~/local/Python3.8/bin/python3 -m venv tensorflow-build-env
git clone https://github.com/tensorflow/tensorflow.git

Cloning into 'tensorflow'... remote: Enumerating objects: 833165, done. remote: Total 833165 (delta 0), reused 0 (delta 0), pack-reused 833165 Receiving objects: 100% (833165/833165), 483.03 MiB | 33.02 MiB/s, done. Resolving deltas: 100% (674581/674581), done. Checking out files: 100% (19594/19594), done.

cd tensorflow
git checkout r1.15

Checking out files: 100% (11771/11771), done. Branch r1.15 set up to track remote branch r1.15 from origin. Switched to a new branch 'r1.15'

. ../tensorflow-build-env/bin/activate
pip install Keras-Preprocessing numpy six wheel

Collecting Keras-Preprocessing Using cached https://files.pythonhosted.org/packages/28/6a/8c1f62c37212d9fc441a7e26736df51ce6f0e38455816445471f10da4f0a/Keras_Preprocessing-1.1.0-py2.py3-none-any.whl Collecting numpy Using cached https://files.pythonhosted.org/packages/41/38/b278d96baebc6a4818cfd9c0fb6f0e62013d5b87374bcf0f14a0e9b83ed5/numpy-1.18.1-cp38-cp38-manylinux1_x86_64.whl Collecting six Using cached https://files.pythonhosted.org/packages/65/eb/1f97cb97bfc2390a276969c6fae16075da282f5058082d4cb10c6c5c1dba/six-1.14.0-py2.py3-none-any.whl Collecting wheel Using cached https://files.pythonhosted.org/packages/8c/23/848298cccf8e40f5bbb59009b32848a4c38f4e7f3364297ab3c3e2e2cd14/wheel-0.34.2-py2.py3-none-any.whl Installing collected packages: numpy, six, Keras-Preprocessing, wheel Successfully installed Keras-Preprocessing-1.1.0 numpy-1.18.1 six-1.14.0 wheel-0.34.2 WARNING: You are using pip version 19.2.3, however version 20.0.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

./configure

WARNING: --batch mode is deprecated. Please instead explicitly shut down your Bazel server using the command "bazel shutdown". You have bazel 0.25.2 installed. Please specify the location of python. [Default is /home/USERNAME/Desktop/tensorflow-issue/tensorflow-build-env/bin/python]:

Found possible Python library paths: /home/USERNAME/Desktop/tensorflow-issue/tensorflow-build-env/lib/python3.8/site-packages Please input the desired Python library path to use. Default is [/home/USERNAME/Desktop/tensorflow-issue/tensorflow-build-env/lib/python3.8/site-packages]

Do you wish to build TensorFlow with XLA JIT support? [Y/n]: XLA JIT support will be enabled for TensorFlow.

Do you wish to build TensorFlow with OpenCL SYCL support? [y/N]: No OpenCL SYCL support will be enabled for TensorFlow.

Do you wish to build TensorFlow with ROCm support? [y/N]: No ROCm support will be enabled for TensorFlow.

Do you wish to build TensorFlow with CUDA support? [y/N]: y CUDA support will be enabled for TensorFlow.

Do you wish to build TensorFlow with TensorRT support? [y/N]: No TensorRT support will be enabled for TensorFlow.

Found CUDA 10.1 in: /usr/local/cuda/lib64 /usr/local/cuda/include Found cuDNN 7 in: /usr/local/cuda/lib64 /usr/local/cuda/include

Please specify a list of comma-separated CUDA compute capabilities you want to build with. You can find the compute capability of your device at: https://developer.nvidia.com/cuda-gpus. Please note that each additional compute capability significantly increases your build time and binary size, and that TensorFlow only supports compute capabilities >= 3.5 [Default is: 6.1,6.1]:

Do you want to use clang as CUDA compiler? [y/N]: nvcc will be used as CUDA compiler.

Please specify which gcc should be used by nvcc as the host compiler. [Default is /usr/bin/gcc]:

Do you wish to build TensorFlow with MPI support? [y/N]: No MPI support will be enabled for TensorFlow.

Please specify optimization flags to use during compilation when bazel option "--config=opt" is specified [Default is -march=native -Wno-sign-compare]:

Would you like to interactively configure ./WORKSPACE for Android builds? [y/N]: Not configuring the WORKSPACE for Android builds.

Preconfigured Bazel build configs. You can use any of the below by adding "--config=<>" to your build command. See .bazelrc for more details. --config=mkl # Build with MKL support. --config=monolithic # Config for mostly static monolithic build. --config=gdr # Build with GDR support. --config=verbs # Build with libverbs support. --config=ngraph # Build with Intel nGraph support. --config=numa # Build with NUMA support. --config=dynamic_kernels # (Experimental) Build kernels into separate shared objects. --config=v2 # Build TensorFlow 2.x instead of 1.x. Preconfigured Bazel build configs to DISABLE default on features: --config=noaws # Disable AWS S3 filesystem support. --config=nogcp # Disable GCP support. --config=nohdfs # Disable HDFS support. --config=noignite # Disable Apache Ignite support. --config=nokafka # Disable Apache Kafka support. --config=nonccl # Disable NVIDIA NCCL support. Configuration finished

bazel build --config=opt --config=cuda //tensorflow/tools/pip_package:build_pip_package

Starting local Bazel server and connecting to it... WARNING: The following configs were expanded more than once: [cuda, using_cuda]. For repeatable flags, repeats are counted twice and may lead to unexpected behavior. INFO: Options provided by the client: Inherited 'common' options: --isatty=1 --terminal_columns=160 INFO: Reading rc options for 'build' from /home/USERNAME/Desktop/tensorflow-issue/tensorflow/.bazelrc: 'build' options: --apple_platform_type=macos --define framework_shared_object=true --define open_source_build=true --define=use_fast_cpp_protos=true --define=allow_oversize_protos=true --spawn_strategy=standalone -c opt --announce_rc --define=grpc_no_ares=true --define=PREFIX=/usr --define=LIBDIR=$(PREFIX)/lib --define=INCLUDEDIR=$(PREFIX)/include --copt=-w --config=v1 INFO: Reading rc options for 'build' from /home/USERNAME/Desktop/tensorflow-issue/tensorflow/.tf_configure.bazelrc: 'build' options: --action_env PYTHON_BIN_PATH=/home/USERNAME/Desktop/tensorflow-issue/tensorflow-build-env/bin/python --action_env PYTHON_LIB_PATH=/home/USERNAME/Desktop/tensorflow-issue/tensorflow-build-env/lib/python3.8/site-packages --python_path=/home/USERNAME/Desktop/tensorflow-issue/tensorflow-build-env/bin/python --config=xla --action_env CUDA_TOOLKIT_PATH=/usr/local/cuda --action_env TF_CUDA_COMPUTE_CAPABILITIES=6.1,6.1 --action_env LD_LIBRARY_PATH=:/usr/local/cuda/lib64 --action_env GCC_HOST_COMPILER_PATH=/usr/bin/gcc --config=cuda --action_env TF_CONFIGURE_IOS=0 INFO: Found applicable config definition build:v1 in file /home/USERNAME/Desktop/tensorflow-issue/tensorflow/.bazelrc: --define=tf_api_version=1 --action_env=TF2_BEHAVIOR=0 INFO: Found applicable config definition build:xla in file /home/USERNAME/Desktop/tensorflow-issue/tensorflow/.bazelrc: --action_env=TF_ENABLE_XLA=1 --define=with_xla_support=true INFO: Found applicable config definition build:xla in file /home/USERNAME/Desktop/tensorflow-issue/tensorflow/.tf_configure.bazelrc: --define with_xla_support=true INFO: Found applicable config definition build:cuda in file /home/USERNAME/Desktop/tensorflow-issue/tensorflow/.bazelrc: --config=using_cuda --define=using_cuda_nvcc=true INFO: Found applicable config definition build:using_cuda in file /home/USERNAME/Desktop/tensorflow-issue/tensorflow/.bazelrc: --define=using_cuda=true --action_env TF_NEED_CUDA=1 --crosstool_top=@local_config_cuda//crosstool:toolchain INFO: Found applicable config definition build:opt in file /home/USERNAME/Desktop/tensorflow-issue/tensorflow/.tf_configure.bazelrc: --copt=-march=native --copt=-Wno-sign-compare --host_copt=-march=native --define with_default_optimizations=true INFO: Found applicable config definition build:cuda in file /home/USERNAME/Desktop/tensorflow-issue/tensorflow/.bazelrc: --config=using_cuda --define=using_cuda_nvcc=true INFO: Found applicable config definition build:using_cuda in file /home/USERNAME/Desktop/tensorflow-issue/tensorflow/.bazelrc: --define=using_cuda=true --action_env TF_NEED_CUDA=1 --crosstool_top=@local_config_cuda//crosstool:toolchain INFO: An error occurred during the fetch of repository 'io_bazel_rules_docker' INFO: Call stack for the definition of repository 'io_bazel_rules_docker':

  • /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/bazel_toolchains/repositories/repositories.bzl:37:9
  • /home/USERNAME/Desktop/tensorflow-issue/tensorflow/WORKSPACE:35:1 ERROR: error loading package '': Encountered error while reading extension file 'repositories/repositories.bzl': no such package '@io_bazel_rules_docker//repositories': Traceback (most recent call last): File "/home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/bazel_tools/tools/build_defs/repo/git.bzl", line 234 _clone_or_update(ctx) File "/home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/bazel_tools/tools/build_defs/repo/git.bzl", line 74, in _clone_or_update fail(("error cloning %s:\n%s" % (ctx....))) error cloning io_bazel_rules_docker:
  • cd /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external
  • rm -rf /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker
  • git clone '' https://github.com/bazelbuild/rules_docker.git /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker Too many arguments.

usage: git clone [options] [--] <repo> [<dir>]

-v, --verbose         be more verbose
-q, --quiet           be more quiet
--progress            force progress reporting
-n, --no-checkout     don't create a checkout
--bare                create a bare repository
--mirror              create a mirror repository (implies bare)
-l, --local           to clone from a local repository
--no-hardlinks        don't use local hardlinks, always copy
-s, --shared          setup as shared repository
--recursive           initialize submodules in the clone
--recurse-submodules  initialize submodules in the clone
--template <template-directory>
                      directory from which templates will be used
--reference <repo>    reference repository
-o, --origin <name>   use <name> instead of 'origin' to track upstream
-b, --branch <branch>
                      checkout <branch> instead of the remote's HEAD
-u, --upload-pack <path>
                      path to git-upload-pack on the remote
--depth <depth>       create a shallow clone of that depth
--single-branch       clone only one branch, HEAD or --branch
--separate-git-dir <gitdir>
                      separate git dir from working tree
-c, --config <key=value>
                      set config inside the new repository
  • git clone https://github.com/bazelbuild/rules_docker.git /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker
  • git -C /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker reset --hard 251f6a68b439744094faff800cd029798edf9faa Unknown option: -C usage: git [--version] [--help] [-c name=value] [--exec-path[=<path>]] [--html-path] [--man-path] [--info-path] [-p|--paginate|--no-pager] [--no-replace-objects] [--bare] [--git-dir=<path>] [--work-tree=<path>] [--namespace=<name>] <command> [<args>]
  • git -C /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker fetch '' origin 251f6a68b439744094faff800cd029798edf9faa:251f6a68b439744094faff800cd029798edf9faa Unknown option: -C usage: git [--version] [--help] [-c name=value] [--exec-path[=<path>]] [--html-path] [--man-path] [--info-path] [-p|--paginate|--no-pager] [--no-replace-objects] [--bare] [--git-dir=<path>] [--work-tree=<path>] [--namespace=<name>] <command> [<args>]
  • git -C /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker fetch origin 251f6a68b439744094faff800cd029798edf9faa:251f6a68b439744094faff800cd029798edf9faa Unknown option: -C usage: git [--version] [--help] [-c name=value] [--exec-path[=<path>]] [--html-path] [--man-path] [--info-path] [-p|--paginate|--no-pager] [--no-replace-objects] [--bare] [--git-dir=<path>] [--work-tree=<path>] [--namespace=<name>] <command> [<args>] ERROR: error loading package '': Encountered error while reading extension file 'repositories/repositories.bzl': no such package '@io_bazel_rules_docker//repositories': Traceback (most recent call last): File "/home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/bazel_tools/tools/build_defs/repo/git.bzl", line 234 _clone_or_update(ctx) File "/home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/bazel_tools/tools/build_defs/repo/git.bzl", line 74, in _clone_or_update fail(("error cloning %s:\n%s" % (ctx....))) error cloning io_bazel_rules_docker:
  • cd /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external
  • rm -rf /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker
  • git clone '' https://github.com/bazelbuild/rules_docker.git /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker Too many arguments.

usage: git clone [options] [--] <repo> [<dir>]

-v, --verbose         be more verbose
-q, --quiet           be more quiet
--progress            force progress reporting
-n, --no-checkout     don't create a checkout
--bare                create a bare repository
--mirror              create a mirror repository (implies bare)
-l, --local           to clone from a local repository
--no-hardlinks        don't use local hardlinks, always copy
-s, --shared          setup as shared repository
--recursive           initialize submodules in the clone
--recurse-submodules  initialize submodules in the clone
--template <template-directory>
                      directory from which templates will be used
--reference <repo>    reference repository
-o, --origin <name>   use <name> instead of 'origin' to track upstream
-b, --branch <branch>
                      checkout <branch> instead of the remote's HEAD
-u, --upload-pack <path>
                      path to git-upload-pack on the remote
--depth <depth>       create a shallow clone of that depth
--single-branch       clone only one branch, HEAD or --branch
--separate-git-dir <gitdir>
                      separate git dir from working tree
-c, --config <key=value>
                      set config inside the new repository
  • git clone https://github.com/bazelbuild/rules_docker.git /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker
  • git -C /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker reset --hard 251f6a68b439744094faff800cd029798edf9faa Unknown option: -C usage: git [--version] [--help] [-c name=value] [--exec-path[=<path>]] [--html-path] [--man-path] [--info-path] [-p|--paginate|--no-pager] [--no-replace-objects] [--bare] [--git-dir=<path>] [--work-tree=<path>] [--namespace=<name>] <command> [<args>]
  • git -C /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker fetch '' origin 251f6a68b439744094faff800cd029798edf9faa:251f6a68b439744094faff800cd029798edf9faa Unknown option: -C usage: git [--version] [--help] [-c name=value] [--exec-path[=<path>]] [--html-path] [--man-path] [--info-path] [-p|--paginate|--no-pager] [--no-replace-objects] [--bare] [--git-dir=<path>] [--work-tree=<path>] [--namespace=<name>] <command> [<args>]
  • git -C /home/USERNAME/.cache/bazel/_bazel_USERNAME/5aa6c3674f37090388bbfbf0ef73a503/external/io_bazel_rules_docker fetch origin 251f6a68b439744094faff800cd029798edf9faa:251f6a68b439744094faff800cd029798edf9faa Unknown option: -C usage: git [--version] [--help] [-c name=value] [--exec-path[=<path>]] [--html-path] [--man-path] [--info-path] [-p|--paginate|--no-pager] [--no-replace-objects] [--bare] [--git-dir=<path>] [--work-tree=<path>] [--namespace=<name>] <command> [<args>] INFO: Elapsed time: 5.267s INFO: 0 processes. FAILED: Build did NOT complete successfully (0 packages loaded)
odinsbane

comment created time in a month

issue openedtensorflow/tensorflow

Unable to build r1.15 using gcc 4.8.5-39 because of -std=c++14 argument.

The crux of this issue is Does tensorflow r1.15 compile with gcc 4.8.5 when I check out r1.15, I cannot compile due to an invalid argument "-std=c++14" similar to #31760 but I do not understand the resolution from that.

I am preparing to migrate to version 2.X so I tried to build r1.15. I get two errors.

The first error is resolved in #28824

The second error I have not gotten around. Everthing seems to build fine then I get.

ERROR: /home/username/.cache/bazel/_bazel_smithm3/6bda0689d89415301f8ee7c16fbd66e8/external/local_config_mlir/BUILD:418:1: C++ compilation of rule '@local_config_mlir//:Support' failed (Exit 1)
gcc: error: unrecognized command line option '-std=c++14'

System information

  • Centos7
  • checkout r1.15 and v1.15.1
  • Python 3.8.1
  • Bazel version 0.25.2
  • GCC/Compiler version 4.8.5-039
  • CUDA/cuDNN version 10.1/7
  • GPU model and memory Nvidia 1080Ti

This appears to be caused by mlir requiring a newer version of gcc, since it requires -std=c++14 and if you replace it with it with '-std=c++1y' you'lll get an error about std::make_unique

Is tensorflow r1.15 supposed to be compatible with gcc 4.8.5 (default on centos 7)?

Reproducing the problem.

git clone https://github.com/tensorflow/tensorflow.git cd tensorflow git checkout r1.15 ./configure Select default options + CUDA bazel build //tensorflow/tools/pip_package:build_pip_package

created time in a month

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha a347c2d596a757834fda1ad0b90d41240b762e8d

Added a method for collecting all of the external forces. Added a method for showing force vectors.

view details

push time in 2 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 27d2c25d83f2d69a2c188c2d14467179d75750ef

Working on a force visualization. Made a bunch of constructor overloads for the Array.

view details

push time in 2 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 335a1ce4141758b8a3edc8f9f3e3f4364f8ca8e1

The texturedplanedataobject now extends the deforming mesh data object, and can be a drop in replacement.

view details

m smith

commit sha 7030aa50f3841c8fa0827447151cb24b7517c6a4

Improved some of the default classes in the javascript bindings. Added a new Arrow data object for displaying on-screen vectors.

view details

push time in 2 months

push eventodinsbane/JLinkExamples

m smith

commit sha 8734482cc81c9d7c623df7950d3e6328021c9648

Created a working window that contains sub windows. Can be used for monitoring log files with a [[data]] format.

view details

m smith

commit sha 5a5dba2b80afe28569b0b8449ff23da03e7f7d11

adding more files from previous commit.

view details

push time in 2 months

issue openedmatplotlib/matplotlib

Call to input blocks slider input on osx with the default agg 'MacOSX'. It works fine on when TkAgg is used.

Bug report

Bug summary I recently updated to matplotlib==3.1.1 and when I use the default backend on OS X, I cannot use non-blocking with the python function input.

#!/usr/bin/env python3

from matplotlib import pyplot
from matplotlib.widgets import Slider
import numpy

figure = pyplot.figure(0)
plot = pyplot.imshow(numpy.random.random((64, 64)))
pyplot.subplots_adjust(left=0.1, bottom=0.25)
axrs = pyplot.axes([0.2, 0.05, 0.65, 0.05], facecolor="blue")
slider = Slider(axrs, "Slice", 0, 3, valinit=1, valstep=1)

def setSlice(slc):
    plot.set_data(numpy.random.random((64, 64)))
    figure.canvas.draw()
slider.on_changed(setSlice)

pyplot.show(block=False)
input("true")

If I run that code, the slider is no longer interactive at all. If I set the MPLBACKEND to be TkAgg, then it works as expected. If I use pyplot.show(block=True) then everything works as expected: the slider changes and the image updates.

I have also tried using:

pyplot.ion()
pyplot.show()
input("waiting")

I get the same behavior.

I am using the slider to select z slices, and I wait on user input to decide to move on to another dataset, so the .show() with block doesn't really help me. Currently my TkAgg work around is sufficient, but I reported this bug in case it is a bug you want to know about, or I am incorrectly showing a non-blocking window.

  • Operating system: MacOS Sierra 10.12.6
  • Matplotlib version: 3.1.1
  • Matplotlib backend (MacOSX):
  • Python version: 3.6.9

I installed using the default anaconda channel. I just updated conda which is how I noticed the error. <!--If you installed from conda, please specify which channel you used if not the default-->

created time in 2 months

push eventodinsbane/learning-dominoes

mbs

commit sha aef3f905ab28d3e3d68510dfc807e1bf078f317c

Fixed something in the plot log to make it work. Scaled the display 2x since it is too small on hdpi display.

view details

push time in 2 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 6a1021f99e16bca49308be09c09fde1e892f3da8

updated python reader with commends, removed the + on the open statement and changed from copying the bytes object to using the offset argument of the position.

view details

m smith

commit sha a1458f1bf28c31a3fc75f53daa7fba5cb0a21e15

Added an icon, to be improved. Working on a height-map/energy for accumulating meshes in the simulation. Added a javascript function to the load bindings that rotates 360 degrees and takes a snapshot at each frame.

view details

push time in 2 months

issue openedscijava/scijava-java3d

Rendering a scene offscreen with 2 3d textures only results in 1 texture being shown.

We have a plugin for fiji for 3d segmentations, and I recently added a way to show a second texture, but when I render to offscreen the second texture does not get displayed.

missing-texture

I use an older plugin we developed to render the 3d scene.

I brought this up in case I am missing something or if there is some interest in trying to figure out what is wrong I can make a java3d example.

created time in 2 months

push eventodinsbane/git_n_click

odinsbane

commit sha d1a58087b795517e69a3a2b6f3de60d68133ffee

Updated readme, some of the description was wrong.

view details

push time in 2 months

push eventodinsbane/JLinkExamples

mbs

commit sha d80ef4e223392d26ea34a76d32f24b32ea12cf7a

Transition from windows to widgets since they clutter the desktop.

view details

push time in 2 months

push eventodinsbane/JLinkExamples

msmith

commit sha 23c36f587395b8ea908585de8582f3e5201e7897

Created a window and started migrating to a widget concept. So multiple guages don't occupy to many task slots.

view details

push time in 2 months

create barnchodinsbane/JLinkExamples

branch : widgetwindow

created branch time in 2 months

issue commenttensorflow/tensorflow

Building Tensorflow 1.13 for python 3.8 fails on nullptr conversion.

The documentation here, https://www.tensorflow.org/guide/upgrade says to upgrade to 1.14 for 2.0 migration. Is that the recommended route to upgrade, or is 1.15 preferred? I am not ready to port to 2.X yet, but I would like to be ready to.

On Tue, Jan 14, 2020 at 10:58 PM tensorflow-bot[bot] < notifications@github.com> wrote:

Are you satisfied with the resolution of your issue? Yes https://docs.google.com/forms/d/e/1FAIpQLSfaP12TRhd9xSxjXZjcZFNXPGk4kc1-qMdv3gc6bEP90vY1ew/viewform?entry.85265664=Yes&entry.2137816233=https://github.com/tensorflow/tensorflow/issues/34197 No https://docs.google.com/forms/d/e/1FAIpQLSfaP12TRhd9xSxjXZjcZFNXPGk4kc1-qMdv3gc6bEP90vY1ew/viewform?entry.85265664=No&entry.2137816233=https://github.com/tensorflow/tensorflow/issues/34197

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/tensorflow/tensorflow/issues/34197?email_source=notifications&email_token=AA2NNEOK336NW4AQYEHRMVDQ5Y7SVA5CNFSM4JMB72GKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEI6NWLQ#issuecomment-574413614, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA2NNEMJ7GZ6LGHRA3CBZ4TQ5Y7SVANCNFSM4JMB72GA .

odinsbane

comment created time in 2 months

issue commenttensorflow/tensorflow

build failed with cuda 10.2

I used this "fix" with tensorflow 1.14 and cuda 10.2. It compiled and installed ok, but I cannot run previously working models. I get an out of memory error, or a failed to load CUDNN error. Seems somewhat random which one will occur.

alanpurple

comment created time in 2 months

push eventodinsbane/jfilament

m smith

commit sha 64df4fb3d4accab12b1e8112db636bcd71cbfae6

Updated CanvasView api. (Removed unused import from CurveGeometry that breaks on java 11 !?)

view details

push time in 3 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 192659c8b39f580073cc08a85d019d1b8361c9a7

Can modify mesh now. Added undoable actions.

view details

m smith

commit sha 7e0e278192f82e4d835d356a5379c11d47ec9f14

Added volume contrast dialog to control frame window, and method to controller. Removed some oll button code

view details

m smith

commit sha f940cedc72fb8b606346f06cc6f2c79f828f25e5

added update positions method for refreshing 3d displayed object with the current positions.

view details

m smith

commit sha 6af8cbc63fbdb171f93b0a327c194306572db0c1

Added a rotate view method; Exposed the vdo object.

view details

m smith

commit sha 38a7e61512d622d129c4c779280ec9bbf61696cf

Updated the pick selector api. Added the capability to write pick selectable to data objects.

view details

push time in 3 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha d1e26f486cb853e7db2a135ab64917c33d5c330b

Improved oscillations. Can be turned on or off, and the view can be adjusted with oscillations continuing from there.

view details

push time in 3 months

issue commenttensorflow/tensorflow

build tensorflow from source failed on Linux

I suspect that TF1.14 and cuda 9.1 are not compatible. I have the same issue currently, and I am trying to switch to 10.1 to see if it builds. I think this issue is actually why I have been using TF 1.13.

dongxiao92

comment created time in 3 months

push eventodinsbane/JLinkExamples

m smith

commit sha b83510e55243d1377f63cb31f642dfc874213312

Got sensorplotting working.

view details

push time in 3 months

push eventodinsbane/JLinkExamples

m smith

commit sha bacca95603f1e0109315078440fd09737114cf68

Setup the hello-world example.

view details

push time in 3 months

create barnchodinsbane/JLinkExamples

branch : master

created branch time in 3 months

created repositoryodinsbane/JLinkExamples

Hello World level jlink examples.

created time in 3 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha 99664f9ca78a97faf17b1667317bb235118e4ed6

Migrated the meshframe3d from having a ThreeDVolume surface to a volume data object. Could be improved yet. Added a check for null on the MeshImageStack when getting the size in px.

view details

push time in 3 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha 8c44ee7be170905f744e9b815711076ef5c53b4a

Creating a volume constrast setter that works with a volume data object, creates a preview where the volume contrast can be adjusted.

view details

push time in 3 months

push eventodinsbane/jfilament

msmith

commit sha fdebef4a6b376a9c2d43eacaed8f732b783aea5e

Changes to make viewer more ammenable to a 3d volume data object.

view details

push time in 3 months

push eventodinsbane/jfilament

m smith

commit sha daf1c9971292206f2ec7968ea205505412912415

Added a method for getting the background color. It can be confused with the Swing background color, so now it is called a canvasBackground to indicate the color of the 3d context background object.

view details

m smith

commit sha d013f2c2ce75ec68844d5dc7d499d179d5d9b36a

Merge branch 'developing' of https://github.com/odinsbane/jfilament into developing

view details

push time in 3 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 608478754ed045d4ad536e73d3ec59c530b6b1bf

Creating an interface to adjust the contrast of the 3d volume. Currently pretty ugly, but functional. Includes a sub-volume view as a preview. beg/set background colors for making the contrast config have the same display as the current display. Also migrating away from the 'volume' that is part of the meshframe3d, and instead using a volume data object.

view details

m smith

commit sha 29fd1dd66c6dbcba659757654af3d3d2d96b550f

Merge branch 'development' of https://github.com/PaluchLabUCL/DeformingMesh3D-plugin into development

view details

push time in 3 months

push eventodinsbane/jfilament

msmith

commit sha 2ab886edfa2f8179a667222b03ee9ff0d5632c10

Working on making the CanvasController allow other interactions.

view details

push time in 3 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha 5fc7866170f5bda3f9df53a82d018f14d0eb600e

working on updating the frame3d to be able to recieve and interact with a mesh for making modifications.

view details

push time in 3 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha ccaf5499b90a4bcb81e1f864aef8db327967b4f1

Connection based remeshing works now.

view details

push time in 4 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 8e6e5a5947f2ee89c76ae38d5cbefe98292c67f4

Volume texture + textured plane is working well. working on removing small connections in the connection remesh algorithm.

view details

push time in 4 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha c720c89cfff556d4bb1ba641928cc4f4b2384f23

Working on generating 3d texture/ arbitrary surface, for surface projections.

view details

push time in 4 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha a3da0fecabacfa0858a2bc689f780324a0156b5c

Working on steric interactions.

view details

m smith

commit sha 76c2f18301d39f5a3e0162e082643b73a994ce83

Merge branch 'development' of https://github.com/PaluchLabUCL/DeformingMesh3D-plugin into development

view details

m smith

commit sha 5acba3fea0cb793afc0c0789689b2646a81df978

Working on geting 3d textured surfaces to work as data object. Debuggins in progress.

view details

push time in 4 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

msmith

commit sha 52aeb9bb815d9397e720405edc7f6f65d7aa4a6b

Creating a "shell mesh" that is a set of complimentary triangles, a set at the original position, and a set at a position displaced along the normal some thickness.

view details

push time in 4 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha b040cc9934a0fb515556c2fce216a85498fbdbb2

created a wireframe mesh for exporting to a triangle file for 3d printing.

view details

push time in 4 months

issue commenttensorflow/tensorflow

Could not create cudnn handle: CUDNN_STATUS_INTERNAL_ERROR

@sanjoy I have a version that exhibits this problem. How would I go about accessing MinSystemMemory or "setting the magic 0.05 number"? I have reverted to using cuda 9.1 for the most part, but I don't mind trying a few things.

6etacat

comment created time in 4 months

issue openedtensorflow/tensorflow

Building Tensorflow 1.13 for python 3.8 fails on nullptr conversion.

System information

  • OS Platform and Distribution: Centos 7
  • TensorFlow installed from : source
  • TensorFlow version: 1.13.2
  • Python version: 3.8.0
  • Bazel version : 0.21.0
  • GCC/Compiler version : gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
  • CUDA/cuDNN version: 9.1/7.0
  • GPU model and memory: 1080ti

Describe the problem

When attempting to build the tensorflow branch r1.13 targeting python 3.8 the build fails with the following error:

ndarray_tensor_bridge.cc:108:1: error: cannot convert 'std::nullptr_t' to 'Py_ssize_t {aka long int}' in initialization };

This error occurs in three files that I found: bfloat16.cc, ndarray_tensor_bridge.cc, pywrap_tfe_src.cc

This appears to be the same problem fixed in issue #33543

Provide the exact sequence of commands / steps that you executed before running into the problem

I am willing to provide more details, but this appears to be the exact same issue. I am including the git diff from the version that compiled and works for me.

diff --git a/tensorflow/python/eager/pywrap_tfe_src.cc b/tensorflow/python/eager/pywrap_tfe_src.cc
index 9ce500b..726c4c5 100644
--- a/tensorflow/python/eager/pywrap_tfe_src.cc
+++ b/tensorflow/python/eager/pywrap_tfe_src.cc
@@ -1216,7 +1216,7 @@ static PyTypeObject TFE_Py_Tape_Type = {
     sizeof(TFE_Py_Tape),                          /* tp_basicsize */
     0,                                            /* tp_itemsize */
     &TFE_Py_Tape_Delete,                          /* tp_dealloc */
-    nullptr,                                      /* tp_print */
+    NULL,                                         /* tp_print */
     nullptr,                                      /* tp_getattr */
     nullptr,                                      /* tp_setattr */
     nullptr,                                      /* tp_reserved */
diff --git a/tensorflow/python/lib/core/bfloat16.cc b/tensorflow/python/lib/core/bfloat16.cc
index fde3a83..e0da0f4 100644
--- a/tensorflow/python/lib/core/bfloat16.cc
+++ b/tensorflow/python/lib/core/bfloat16.cc
@@ -317,7 +317,7 @@ PyTypeObject PyBfloat16_Type = {
     sizeof(PyBfloat16),                        // tp_basicsize
     0,                                         // tp_itemsize
     nullptr,                                   // tp_dealloc
-    nullptr,                                   // tp_print
+    NULL,                                      // tp_print
     nullptr,                                   // tp_getattr
     nullptr,                                   // tp_setattr
     nullptr,                                   // tp_compare / tp_reserved
diff --git a/tensorflow/python/lib/core/ndarray_tensor_bridge.cc b/tensorflow/python/lib/core/ndarray_tensor_bridge.cc
index 0d58385..43ab92c 100644
--- a/tensorflow/python/lib/core/ndarray_tensor_bridge.cc
+++ b/tensorflow/python/lib/core/ndarray_tensor_bridge.cc
@@ -86,7 +86,7 @@ PyTypeObject TensorReleaserType = {
     0,                                /* tp_itemsize */
     /* methods */
     TensorReleaser_dealloc,      /* tp_dealloc */
-    nullptr,                     /* tp_print */
+    NULL,                        /* tp_print */
     nullptr,                     /* tp_getattr */
     nullptr,                     /* tp_setattr */
     nullptr,                     /* tp_compare */

created time in 5 months

issue commenttensorflow/tensorflow

TF 2.0.0 Python 3.8 TypeError: _logger_find_caller() takes from 0 to 1 positional arguments but 2 were given

I recieved this error also when using tensorflow 1.13.2 + python 3.8 I am considering opening a separate issue.

dbonner

comment created time in 5 months

issue closedPaluchLabUCL/DeformingMesh3D-plugin

Record snapshots is broken when the volume is showing.

The output image is only the first frame.

closed time in 5 months

odinsbane

issue commentPaluchLabUCL/DeformingMesh3D-plugin

Record snapshots is broken when the volume is showing.

I fixed this at some point, probably in JFilament, not excatly sure when though.

odinsbane

comment created time in 5 months

push eventodinsbane/speckletrackerj

m smith

commit sha fc63da881e223689a81d3bc38aa496ccc31023b0

Made the program work again, updated some of the text fields to display since they were hidden before.

view details

push time in 6 months

issue openedspyder-ide/spyder

Trailing spaces are being removed on line change even if the option is unset in preferences.

Problem Description

In the editor, if I move down from an indented line to another indented line, then move back up, the line above is no longer indented.

I tried to disable the option "automatically strip trailing spaces on changed lines" in preferences->editor->source code, but the spaces are still removed.

What steps reproduce the problem?

  1. Create a new function.
  2. Press enter to go to the next line, which should be indented.
  3. Press enter again, to go to a second indented line.
  4. Press up to move back up to the previous line, and it is no longer indented and no longer contains any spaces.

What is the expected output? What do you see instead?

I dont expect the first lines to lose their indentations. If I add "show spaces" I can see the first line losses it's indentations when I press return the second time. I would like.

def main():
    
    

(The spaces are there, but I am not sure of a good way to show them on this interface.)

Quite possibly, I am not setting/unsetting the correct option.

Versions

Spder 4.0.0b5

Python 3.6.8 64-bit
Qt 5.12.4
PyQt5 5.12.3
Linux 3.10.0-1062.el7.x86_64 Centos 7

created time in 6 months

push eventodinsbane/jfilament

m smith

commit sha 7e3a00e4da56fdb1a6a15e17a34cd3ccc5446e53

Errors from javadoc generation. Intellij complained about invalid options in pom.xml

view details

m smith

commit sha 4cc65dd3a0ecf508c9fd20290741f6f161e43a3d

Merge remote-tracking branch 'origin' into developing

view details

push time in 6 months

push eventodinsbane/jfilament

m smith

commit sha 7e3a00e4da56fdb1a6a15e17a34cd3ccc5446e53

Errors from javadoc generation. Intellij complained about invalid options in pom.xml

view details

push time in 7 months

issue closedodinsbane/jfilament

Kimograph plugin doesn't preserve length.

The way the plugin works: It takes one snake from the snake file and goes through all of the points sampling a box oriented along the line segment connecting the two points. Consider the length of a segment, L and the length of a box B, then the relation ship holds that L<=B<=L+1 because, the segments have fraction pixel lengths, but the boxes are integers.

A solution to this would be to move along the curve with a parameter that increments pixel lengths, then samples a width that is parallel to the segment the current position falls on.

If the sampling point landed exactly on a control point the tangent could be ambiguous. Solutions: average tangent. Pick one. Sample both, and average that.

closed time in 7 months

odinsbane

issue commentodinsbane/jfilament

Kimograph plugin doesn't preserve length.

Kimograph2 preserves length. It samples at 1px intervals. Possibly even skipping whole sections if they are shorter than an interval.

odinsbane

comment created time in 7 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 1b5dea2685669a517c6d8dbd1db429f90b260a16

Updated pom file for release.

view details

m smith

commit sha 943a390e8b97c999869781a2a12fd12b238c4250

Changed the jfilament dependency to include 1.1.7 and edu.leghigh for the group id.

view details

m smith

commit sha 88f70ef0d13f069e6841d3ef08222e52b3fb7bd2

Prepared pom for snapshot developing.

view details

push time in 7 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 943a390e8b97c999869781a2a12fd12b238c4250

Changed the jfilament dependency to include 1.1.7 and edu.leghigh for the group id.

view details

push time in 7 months

issue closedodinsbane/jfilament

Create a way to clear the snake in the current frame w/out deleting the whole snake.

Currently to clear a snake from the current frame, you have to make it go away through some sort of deformation/edit it down to nothing.

closed time in 7 months

odinsbane

push eventodinsbane/jfilament

Curtis Rueden

commit sha d8f49bfbba78aa0f6a7977d8aaf3a05d791d1e89

POM: use HTTPS where feasible

view details

odinsbane

commit sha 2c63998aa4a9d9a5fd8b3cd2ac60036375d3b3c1

Merge pull request #5 from ctrueden/use-https Use HTTPS in the POM where feasible

view details

Curtis Rueden

commit sha 15f83506b9d641329f83dc0c1ceba8493ad97c6a

POM: ImageJ Forum -> Image.sc Forum

view details

Curtis Rueden

commit sha 671de15d53e968517aca8df6222ef3e9ac3837c1

POM: maven.imagej.net -> maven.scijava.org

view details

Curtis Rueden

commit sha d18a10e5df6be5871c35ccfa784b73365849a60a

Travis: build using openjdk8

view details

odinsbane

commit sha d78aeefdf42b5dc71acb027956dfc8df98a280fb

Merge pull request #6 from ctrueden/imagej-to-scijava Update to SciJava Maven repository

view details

m smith

commit sha f53fef61bd7fbbef5c809f78037c865d02cad6bc

updated pom to represent release, updateded readme to include changes.

view details

m smith

commit sha e9c9d65d01911ee913903311564d278950c68462

Merge branch 'master' of https://github.com/odinsbane/jfilament

view details

m smith

commit sha f87e1b2b27c575d4507b105976fba133b922d54d

Starting 1.1.8 development cycle.

view details

push time in 7 months

push eventodinsbane/jfilament

m smith

commit sha add2fff9f41da89bc105380100c0377315d07c52

updated versions to next snapshot.

view details

m smith

commit sha 95697d1aded4b138694009c5de0a1f94ef8ea6fe

Spelling change

view details

msmith

commit sha 51def72a4c4cf8abf4be0e9a0d5af3eedd39bcae

Creating a method for creating a binary mask from snakes.

view details

m smith

commit sha 24dde05f4d1cfc8ec05cb82f521fa8dcf48e24c8

BUG FIX: Taking a snapshot no longer breaks if there is a volume showing. Created a look at method, or specifying an up and normal for viewing.

view details

m smith

commit sha 1ead19588e04e31540b9595ea8643f8a33669f63

Merge branch 'developing' of https://github.com/odinsbane/jfilament into developing

view details

m smith

commit sha d1ce747cb28557ba743720e25cd250813693a148

Updated the drawing so for a bug fix when 'deleting' a snake by editing it away. Updated the curve geometry.

view details

m smith

commit sha 86ce65515eed0a0dff48d02062b598a8d2275f23

Added a method to clear the currently selected snake from the current frame only.

view details

m smith

commit sha f53fef61bd7fbbef5c809f78037c865d02cad6bc

updated pom to represent release, updateded readme to include changes.

view details

m smith

commit sha e9c9d65d01911ee913903311564d278950c68462

Merge branch 'master' of https://github.com/odinsbane/jfilament

view details

push time in 7 months

push eventodinsbane/jfilament

m smith

commit sha 86ce65515eed0a0dff48d02062b598a8d2275f23

Added a method to clear the currently selected snake from the current frame only.

view details

push time in 7 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 3aac602212d832a42369284ab165d5561e72e034

Updated version to development.

view details

m smith

commit sha 5a1915bed2286e29e700a7cfdc6a5218d8a36f4e

BUG FIX: Issue #5.

view details

m smith

commit sha 9722d0dcd8dba146f7267607433f0c4930c59b8b

Added a rigid boundary mode, with checkbox, for preventing the mesh from leaving the bounds of the image.

view details

m smith

commit sha a96d0cd896c4561a6c418898d1ca05cb72d4eca2

The reader was broken, and the endianedness was default. Set to big-endian and it works for a test mesh.

view details

mbs

commit sha 9b3c456271e26286b151f6744da35f17a7fb76de

updated two drops simulation such that the steric mesh updates shape. Also tried a "sticky mesh" technique.

view details

m smith

commit sha 2897c94a170eb75d47da54cc534df736ca918b3a

Minor changes preparing for a merge.

view details

m smith

commit sha e1f92f772bc2d9f6018557b7c34391f68c267927

Merge branch 'development' of https://github.com/PaluchLabUCL/DeformingMesh3D-plugin into development

view details

m smith

commit sha 163567ce9d160c55eb9f820f8d88b87860ed108c

Added a method for performing some curvature analysis. Some work on interacting meshes.

view details

m smith

commit sha aff6f6955097ae30f3c297f1e7d9a51ce98ec089

Added lightgraph to the dependencies.

view details

msmith

commit sha cdf91d9f210b48a3b6f5f386dfb9d4f52a30516e

working on improving the lighting. Forgot to turn on the lighting in the plugin start.

view details

msmith

commit sha 808c65dcd84372261f04cc282bb0873e91a51538

Added some ways to adjust the lighting through the javascript console.

view details

msmith

commit sha cd4efb463be0209bdc1ee18c4f426c96e92ffe28

updated readme. added a set volume color. added example to readme.md

view details

m smith

commit sha 97f05ffb2596f88dc701d079adcaa2a8b3762ed8

Added the steric meshes to deforming, the javascript console is required for using the feature.

view details

m smith

commit sha da75452f4df6ac2bc6289cb3bc3959942bac7055

Merge branch 'development' of https://github.com/PaluchLabUCL/DeformingMesh3D-plugin into development forgotten changes on the server.

view details

msmith

commit sha 68238350e166f20cc481b804a8ddcf9a2650a314

Fixed the 3D cursor in the furrow initialization dialog.

view details

m smith

commit sha 09d4d50194cedcd1ca076578d21bf7f80bd59fbd

Created a way to fill binary blobs.

view details

m smith

commit sha fe6b40bf16dd8c3e778f922ebe19a36a3604a377

Merge branch 'development' of https://github.com/PaluchLabUCL/DeformingMesh3D-plugin into development

view details

m smith

commit sha 4ad575087cecd5d8028929cd914e1f541cedaf52

Updating curvature calculations. Changed the 3d axis to look a bit more informative.

view details

m smith

commit sha d820dcd3ad722ca4408640d9dc7a930e7e49c4ff

Created 3D surface plots, curvature and intensity. BUG FIX: choosed unused color for track.

view details

m smith

commit sha 4b6dcb85c9e51a31bb57a94e24b29b8f2a37351d

Commented the segmentation controller.

view details

push time in 7 months

push eventPaluchLabUCL/DeformingMesh3D-plugin

m smith

commit sha 97985ce59bed1ea02cc60e92aba0c64dc0488616

Made the steric energy react perpendicular to the surface.

view details

m smith

commit sha e8777148e8faa033caaf6d66d8ec09a52b4096af

normal steric force was broken. current method, find the normal, and direction from the center. If they're aligned, then the mesh expands (the other mesh is 'inside') if they're anti-aligned then the deforming mesh shrinks. Can be inverted by using a negative number.

view details

m smith

commit sha 636c702799db24d0d76fee93bcb9518097f94e97

Updated readme to include some instructions and links, updated a method name on the surface plot.

view details

push time in 7 months

push eventodinsbane/jfilament

m smith

commit sha d1ce747cb28557ba743720e25cd250813693a148

Updated the drawing so for a bug fix when 'deleting' a snake by editing it away. Updated the curve geometry.

view details

push time in 7 months

more