For python 3.7+
Creating an environment:
conda create -n my_env python=3.7
conda activate my_env
conda install -c conda-forge/label/gcc7 z5py
conda install -c conda-forge pytables
pip install -r requirementsusage: fetch_mesh.py [-h] -c CREDENTIALS -o OUTPUT [-s STACK_ID] volume
positional arguments:
volume Name or ID of CATMAID volume for which to fetch a mesh
optional arguments:
-h, --help show this help message and exit
-c CREDENTIALS, --credentials CREDENTIALS
Path to JSON file containing CATMAID credentials (as
accepted by catpy)
-o OUTPUT, --output OUTPUT
Output file.
-s STACK_ID, --stack_id STACK_ID
If stack ID is passed, convert the mesh into stack
coordinates
usage: training_data.py [-h] -c CREDENTIALS -o OUTPUT -s STACK_ID [-n]
[-p PAD_XY] [-z PAD_Z]
roi [roi ...]
positional arguments:
roi Any number of ROIs, each passed in as a JSON string
encoding a list of 2 lists of 3 integers. e.g.
'[[1991,20000,12000],[2007,20200,12200]]'
optional arguments:
-h, --help show this help message and exit
-c CREDENTIALS, --credentials CREDENTIALS
Path to JSON file containing CATMAID credentials (as
accepted by catpy)
-o OUTPUT, --output OUTPUT
Output file(s). Can either be passed several times,
once for each input ROI, or passed once as a format
string (e.g. data{}.hdf5)
-s STACK_ID, --stack_id STACK_ID
Stack ID from which to get images
-n, --connector_nodes
Whether to include a volume with connector node
locations in the output
-p PAD_XY, --pad_xy PAD_XY
Number of pixels to pad on both sides in X and Y,
default 100
-z PAD_Z, --pad_z PAD_Z
Number of slices to pad on both sides in Z, default 8