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Boss Upload Cutout Tutorial
Tim Gion edited this page Nov 1, 2016
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Before uploading cutout data, make sure you can answer yes to the following questions.
Cutout checklist:
- Is the cutout within the dimensions of the experiment's coordinate frame?
- Does the data's type match the data type of the channel or layer?
- Is the
numpy
array arranged properly (Z-Y-X or time-Z-Y-X)? - Are the coordinate ranges specified using Python's range convention (second number is the stop value)?
This tutorial uses the collection and experiment shown in the [Boss Project Setup](https://github.com/jhuapl-boss/intern/wiki/Boss Project Setup Tutorial) tutorial.
from intern.remote.boss import BossRemote
from intern.resource.boss.resource import *
import numpy
rmt = BossRemote()
COLL_NAME = 'JHUAPL'
EXP_NAME = 'Mouse17'
CHAN_NAME = 'EM2'
# Create a new channel that uses uint16 data.
chan_setup = ChannelResource(CHAN_NAME, COLL_NAME, EXP_NAME, 'image', datatype='uint16')
chan = rmt.create_project(chan_setup)
# Ranges use the Python convention where the second number is the stop
# value. Thus, x_rng specifies x values where: 0 <= x < 8.
x_rng = [0, 8]
y_rng = [0, 4]
z_rng = [0, 5]
# Note that the numpy matrix is in Z, Y, X order.
data = numpy.random.randint(0, 3000, (5, 4, 8))
# Make data match what was specified for the channel.
data = data.astype(numpy.uint16)
# Upload the cutout to the channel. The zero parameter specifies native
# resolution.
rmt.create_cutout(chan, 0, x_rng, y_rng, z_rng, data)
Table of Contents:
- Overview
- Installation
- Get started
- Boss
- Boss Bounding Box Tutorial
- Boss Download Cutout Tutorial
- Boss Examples
- Boss Ids in Region Tutorial
- Boss Project Auth Tutorial
- Boss Project Metadata Tutorial
- Boss Project Setup Tutorial
- Boss Reserve Ids Tutorial
- Boss Setup Tutorial
- Boss Tutorials
- Boss Upload Cutout Tutorial
- Boss User Management Tutorial
- Dvid
- HDF5