A collection of utility functions for dealing with dvid data
conda install -c flyem-forge dvidutils
In [1]: import numpy as np
In [2]: from dvidutils import LabelMapper, downsample_labels
In [3]: labels = np.random.randint(0, 3, (9,9), dtype=np.uint64)
In [4]: labels
Out[4]:
array([[2, 0, 0, 0, 1, 0, 1, 0, 1],
[1, 1, 1, 2, 1, 0, 2, 2, 2],
[1, 2, 2, 1, 1, 2, 1, 1, 2],
[0, 2, 1, 0, 1, 0, 2, 0, 2],
[2, 2, 1, 0, 0, 0, 1, 2, 1],
[0, 1, 0, 1, 2, 2, 2, 2, 0],
[0, 0, 2, 2, 1, 2, 1, 0, 2],
[2, 0, 2, 1, 2, 2, 2, 2, 1],
[1, 1, 1, 1, 2, 0, 2, 0, 1]], dtype=uint64)
In [5]: mapping = {1:10, 2:20}
In [6]: mapping_keys = np.array( list(mapping.keys()), np.uint64 )
In [7]: mapping_values = np.array( list(mapping.values()), np.uint64 )
In [8]: mapper = LabelMapper(mapping_keys, mapping_values)
In [9]: remapped = mapper.apply( labels, allow_unmapped=True )
In [10]: remapped
Out[10]:
array([[20, 0, 0, 0, 10, 0, 10, 0, 10],
[10, 10, 10, 20, 10, 0, 20, 20, 20],
[10, 20, 20, 10, 10, 20, 10, 10, 20],
[ 0, 20, 10, 0, 10, 0, 20, 0, 20],
[20, 20, 10, 0, 0, 0, 10, 20, 10],
[ 0, 10, 0, 10, 20, 20, 20, 20, 0],
[ 0, 0, 20, 20, 10, 20, 10, 0, 20],
[20, 0, 20, 10, 20, 20, 20, 20, 10],
[10, 10, 10, 10, 20, 0, 20, 0, 10]], dtype=uint64)
In [11]: downsample_labels(remapped, factor=3, suppress_zero=True)
Out[11]:
array([[10, 10, 10],
[10, 10, 20],
[10, 20, 20]], dtype=uint64)Here's how to make an ordinary Makefile-based build:
conda install -c conda-forge python=3.6 cmake xtensor-python
mkdir build
cd build
# Makefiles
cmake .. \
-DCMAKE_BUILD_TYPE=Debug \
-DCMAKE_CXX_FLAGS_DEBUG="-g -O0 -DXTENSOR_ENABLE_ASSERT=ON" \
-DCMAKE_PREFIX_PATH="${CONDA_PREFIX}" \
##
make
make install
Note: Requires gcc >=4.9 or a recent version of clang. On CentOS, the easiesst way to get gcc-4.9 is with these commands:
# Install devtoolset-3
yum install -y centos-release-scl yum-utils devtoolset-3-binutils devtoolset-3-gcc devtoolset-3-gcc-c++
# Activate it (preferably in your .bashrc)
source /opt/rh/devtoolset-3/enable
On Mac, your best option for C++14 development is to use Xcode. (On Linux, your best option is to switch to Mac.)
To use Xcode and its debugger, add -G Xcode to the cmake command:
cmake .. \
-G Xcode \
-DCMAKE_BUILD_TYPE=Debug \
-DCMAKE_CXX_FLAGS_DEBUG="-g -O0 -DXTENSOR_ENABLE_ASSERT=ON" \
-DCMAKE_PREFIX_PATH="${CONDA_PREFIX}" \
open dvidutils.xcodeproj
Xcode is finicky about which executables it likes. Install this special build of Python:
conda install -c conda-forge python.app
Within Xcode, Opt+click the 'Run' button to edit your executable settings:
- Under "Info":
- Select
${CONDA_PREFIX}/python.appas the Executable (NOT${CONDA_PREFIX}/bin/python.app).
- Select
- Under "Arguments":
- Add an Environment Variable for
PYTHONPATH:/path/to/my-dvidutils-repo/build-for-xcode/Debug - Add an item to "Arguments Passed on Launch":
-m pytest --color=no /path/to/my-dvidutils-repo/tests
- Add an Environment Variable for
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