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will-moore / omero_import.py
Created December 1, 2017 09:57
Python code to import files to OMERO
# From http://www.openmicroscopy.org/community/viewtopic.php?f=6&t=8407
# Uses code from https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/tools/OmeroPy/src/omero/testlib/__init__.py
import omero
import platform
import os
from omero.model import ChecksumAlgorithmI
from omero.model import NamedValue
from omero.model.enums import ChecksumAlgorithmSHA1160
@will-moore
will-moore / set_timestamps.py
Created November 20, 2017 22:30
Set PlaneInfo with deltaT values for an Image in OMERO
import omero
from omero.gateway import BlitzGateway
from omero.model.enums import UnitsTime
from omero.model import PlaneInfoI
from omero.rtypes import rint, unwrap
conn = BlitzGateway("user", "password", host="eel.openmicroscopy.org", port=14064)
@will-moore
will-moore / Add_Metadata.py
Created November 16, 2017 22:22
An OMERO.script for adding metadata to images in OMERO
# See https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8397#p18758
import omero.scripts as scripts
import omero
from omero.gateway import BlitzGateway
from omero.model import InstrumentI, MicroscopeI, ObjectiveSettingsI, ObjectiveI
from omero.rtypes import rstring, rdouble, rlong
@will-moore
will-moore / add_instrument_metadata.py
Created November 13, 2017 13:34
Adding Instrument metadata to an Image in OMERO
# See https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8397#p18758
import omero
from omero.gateway import BlitzGateway
from omero.model import InstrumentI, MicroscopeI, ObjectiveSettingsI, ObjectiveI
from omero.rtypes import rstring, rdouble
conn = BlitzGateway("user", "password", host="server.org", port=4064)
conn.connect()
@will-moore
will-moore / micro-bot-remote.js
Created November 7, 2017 23:55
Micro-bit code for bit-bot controlled via remote
let bend = 0
let speed = 0
radio.onDataPacketReceived( ({ receivedString: name, receivedNumber: value }) => {
if (name == "bend") {
basic.showLeds(`
. . . . .
. # . # .
# # # # #
. # . # .
. . . . .
@will-moore
will-moore / connect_to_remote_omero.py
Last active November 8, 2017 16:25
Tests connecting to a remote OMERO server from within an OMERO.script on a local server.
# From e-mail: http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2017-October/004076.html
# We upload and run an OMERO.script
# that can connect to another remote OMERO server.
from omero.gateway import BlitzGateway
import omero
USERNAME = "root"
  • webgateway/base_site.html
  • webgateway/core_html.html
    • webgateway/base_frame.html
    • webclient/annotations/annotations_share.html *Right panel share NB: metadata_general DOES NOT extend core_html.html
    • webclient/annotations/batch_annotate.html *Right panel
    • webclient/annotations/download_placeholder.html Dialog for original files download
    • webclient/scripts/no_processor.html
    • webclient/scripts/script_ui.html
    • webgateway/viewport/omero_image.html
    • webadmin/forgotten_password.html
@will-moore
will-moore / omero-docker-test.sh
Last active August 22, 2017 11:30
Commands for running OMERO in Docker for testing OMERO.web
# DOCKER OMERO
$ cd Desktop/OMERO-INSTALL/omero-install/
$ git fetch origin
$ git checkout origin/develop
$ cd linux/test
$ ./docker-build.sh ubuntu1604_nginx
...
+ OMEROVER=latest
+ WEBAPPS=false
@will-moore
will-moore / Attach_Original_Metadata.py
Last active September 28, 2021 09:33
OMERO.script that loads Original Metadata (read via BioFormats) and saves this as a text file on the Image so that this becomes indexed by the search engine.
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Create File Annotations from Original Metadata.
See https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=1226
"""
import omero
# Copy the config locally so we don't lose it
cp dist/etc/grid/config.xml config.xml
# Delete all previous symlinks, so that 'clean' doesn't delete src code
rm dist/lib/python/omeroweb
rm dist/lib/python/omero/gateway
rm components/tools/target/lib/python/omeroweb
rm components/tools/target/lib/python/omero/gateway
rm components/tools/OmeroPy/target/omero/testlib/
rm components/tools/OmeroPy/target/omero/gateway