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01-KeyVal_from_Description.py
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01-KeyVal_from_Description.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
MIF/Key_Val_from_FileName.py
Adds key-value (kv) metadata to images in a dataset in two ways:
1. at the file level kv from parsing the filename
2. common set of kv pairs from the dataset desciption
The information is found by parsing the Description text for the data set
-----------------------------------------------------------------------------
Copyright (C) 2018
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
------------------------------------------------------------------------------
@author Christian Evenhuis
<a href="mailto:christian.evenhuis@gmail.com">christian.evenhuis@gmail.com</a>
@version 5.3
@since 5.3
"""
import sys, os
import re
from omero.gateway import BlitzGateway
import omero
from omero.cmd import Delete2
from omero.rtypes import rlong, rstring, robject
import omero.scripts as scripts
import copy
from collections import OrderedDict
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def GetExistingMapAnnotions( obj ):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ord_dict = OrderedDict()
for ann in obj.listAnnotations():
if( isinstance(ann, omero.gateway.MapAnnotationWrapper) ):
kvs = ann.getValue()
for k,v in kvs:
if k not in ord_dict:
ord_dict[k]=set()
ord_dict[k].add(v)
return ord_dict
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def RemoveMapAnnotations(conn, dtype, Id ):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
image = conn.getObject(dtype,int(Id))
namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
filename = image.getName()
anns = list( image.listAnnotations())
mapann_ids = [ann.id for ann in anns
if isinstance(ann, omero.gateway.MapAnnotationWrapper) ]
try:
delete = Delete2(targetObjects={'MapAnnotation': mapann_ids})
handle = conn.c.sf.submit(delete)
conn.c.waitOnCmd(handle, loops=10, ms=500, failonerror=True,
failontimeout=False, closehandle=False)
except Exception as ex:
print("Failed to delete links: {}".format(ex.message))
return
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def AddKeysToMatchingFiles( conn, Id, global_kv, template, file_keys, spec_kv=None ):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataset = conn.getObject("Dataset",Id)
# compile the regexp
if( template is not None ):
template="^{}$".format(template)
template= template.replace("*","([^\s_\/]+)")
template= template.replace("?","[^\s_\/]")
regexp = re.compile(template)
# add the metadata to the images
nimg=dataset.countChildren()
nimg_updated=0
nkv_added=0
for image in dataset.listChildren():
if( not ( image.canAnnotate() and image.canLink() ) ):
message = "You don't have permission to add annotations to {}".format(image.getName())
client.setOutput("Message", rstring(message) )
return
existing_kv = GetExistingMapAnnotions(image)
updated_kv = copy.deepcopy(existing_kv)
for key,vals in global_kv.items():
if key not in updated_kv: updated_kv[key] = set()
for val in vals:
updated_kv[key].add(val)
if( template is not None ):
# apply the template to the file name
name = image.getName()
# this adds directory path to filename
# is probably better to extend name of file with path first
#path = os.path.dirname(image.getImportedImageFilePaths()['client_paths'][0])
#filename = path+"/"+name
filename=name
match = regexp.search(filename)
if( match is not None ):
print("Match found",filename)
for i,val in enumerate(match.groups()):
i1 = i
if( i1 in file_keys ):
key = file_keys[i1]
if key not in updated_kv: updated_kv[key] = set()
updated_kv[key].add(val)
if( spec_kv is not None ):
for key,vals in spec_kv.items():
if key not in updated_kv: updated_kv[key] = set()
for val in vals:
updated_kv[key].add(val)
nold_i = sum(map( len, existing_kv.values()))
nnew_i = sum(map( len, updated_kv.values()))
nkv_added = nkv_added+(nnew_i+nold_i)
if( existing_kv != updated_kv ):
RemoveMapAnnotations( conn, 'image', image.getId() )
map_ann = omero.gateway.MapAnnotationWrapper(conn)
namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
# namespace = "openmicroscopy.org/mapr/gene"
map_ann.setNs(namespace)
# convert the ordered dict to a list of lists
kv_list=[]
for k,vset in updated_kv.items():
for v in vset:
kv_list.append( [k,v] )
map_ann.setValue( kv_list )
map_ann.save()
image.linkAnnotation(map_ann)
nimg_updated = nimg_updated+1
return nimg_updated,nkv_added
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def AddMapAnnotations(conn, dtype, Id ):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
'''
* Reads information from the 'Dataset Details' field,
* constructs key-val data
* attaches it to the dataset and the images contained in it
'''
dataset = conn.getObject(dtype,int(Id))
if( not ( dataset.canAnnotate() and dataset.canLink() ) ):
message = "You don't have permission to add annotations to {}".format(dataset.getName())
client.setOutput("Message", rstring(message) )
return
description = dataset.getDescription().splitlines()
modes ={"Summary" : "default" ,
"global key-value" : "global" ,
"filename key-value" : "filename",
"end key-value" : "default" }
mode = 'default'
global_kv = OrderedDict() # stores the global key value pairs
file_keys = OrderedDict() # stores the 'slot' and key for the file keys
spec_kv = OrderedDict() # stores the file specific kv's
template = None
nimg_updated=0
nkv_updated=0
for line in description:
# 1. See if this is a mode string
match = re.search( "^#\s*(\S+\s+\S+)",line.lower())
if( match is not None and match.group(1) in modes ):
value = modes[match.group(1)]
# start a new filename block
if( mode!='filename' and value=='filename' ):
file_keys = OrderedDict()
spec_kv = OrderedDict()
template = None
# end a filename block
if( mode=='filename' and value!='filename' ):
print("Trigger parse fileanames")
print(spec_kv)
nimg_up,nadd = AddKeysToMatchingFiles( conn, Id, OrderedDict(), template, file_keys, spec_kv )
print("filename {} {}".format(nimg_up,nadd))
nimg_updated=nimg_updated+nimg_up
nkv_updated =nkv_updated +nadd
# end a global block
if( mode=='global' and value!='global' ):
# Add globals to all the images
nimg_up, nadd = AddKeysToMatchingFiles( conn, Id, global_kv, None, file_keys )
print("Global: {} {}".format(nimg_up,nadd))
nimg_updated=nimg_updated+nimg_up
nkv_updated =nkv_updated +nadd
mode = value
if( mode == 'default' ):
pass
if( mode == 'global' ):
# split the line for the kay value pair
match = re.search("^\s*(\S+)\s*:\s*(.*)",line)
if( match is not None ):
key = match.group(1)
val = match.group(2)
if( key not in global_kv ): global_kv[key]=set()
global_kv[key].add(val)
if( mode == 'filename' ):
# the template
match = re.search( "^\s*(\S+)\s+(\S+)",line)
if( match and (match.group(1).lower()=='template') ):
template = match.group(2)
print("New template {}".format(template) )
# file templated kvs
# Start line
# | /----white space
# | |full stop|
# V V V V
match = re.search("^\s*(\d)\.\s+(\S+)",line)
# ^ ^
# position key
if( match is not None ):
i = int(match.group(1))-1
file_keys[i] = match.group(2)
# file specific kvs
match = re.search("^\s*(\S+)\s*:\s*(\S+)",line)
if( match is not None ):
key = match.group(1)
val = match.group(2)
if( key not in spec_kv ): spec_kv[key]=set()
spec_kv[key].add(val)
# now add the key value pairs to the dataset
existing_kv = GetExistingMapAnnotions(dataset)
if( existing_kv != global_kv ):
RemoveMapAnnotations( conn, 'dataset', dataset.getId() )
map_ann = omero.gateway.MapAnnotationWrapper(conn)
namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
# namespace = "openmicroscopy.org/mapr/gene"
map_ann.setNs(namespace)
# convert the ordered dict to a list of lists
kv_list=[]
for k,vset in global_kv.items():
for v in vset:
kv_list.append( [k,v] )
map_ann.setValue( kv_list )
map_ann.save()
dataset.linkAnnotation(map_ann)
# add the metadata to the images
if( True ):
#AddKeysToMatchingFiles( conn, Id, global_kv, template, file_keys )
return "Added a total of {} kv pairs to {}/{} files ".format(nkv_updated,nimg_updated,len(list(dataset.listChildren())))
else:
nimg=dataset.countChildren()
nimg_updated=0
nkv_tot=0
for image in dataset.listChildren():
if( not ( image.canAnnotate() and image.canLink() ) ):
message = "You don't have permission to add annotations to {}".format(image.getName())
client.setOutput("Message", rstring(message) )
return
existing_kv = GetExistingMapAnnotions(image)
updated_kv = copy.deepcopy(global_kv)
if( template is not None ):
# apply the template to the file name
name = image.getName()
path = os.path.dirname(image.getImportedImageFilePaths()['client_paths'][0])
filename = path+"/"+name
match = regexp.search(filename)
if( match is not None ):
for i,val in enumerate(match.groups()):
i1 = i+1
if( i1 in file_keys ):
key = file_keys[i1]
if key not in updated_kv: updated_kv[key] = set()
updated_kv[key].add(val)
print("existing_kv")
for k,v in existing_kv.items():
print(" {} : {}".format(k,v))
print("updated_kv")
for k,v in updated_kv.items():
print(" {} : {}".format(k,v))
print("Are they the same?",existing_kv == updated_kv )
if( existing_kv != updated_kv ):
print("The key-values pairs are different")
RemoveMapAnnotations( conn, 'image', image.getId() )
map_ann = omero.gateway.MapAnnotationWrapper(conn)
# namespace ="openmicroscopy.org/mapr/gene"
map_ann.setNs(namespace)
print("Namespace")
print(map_ann)
# convert the ordered dict to a list of lists
kv_list=[]
for k,vset in updated_kv.items():
for v in vset:
kv_list.append( [k,v] )
map_ann.setValue( kv_list )
map_ann.save()
image.linkAnnotation(map_ann)
nimg_updated=nimg_updated+1
nkv_tot = nkv_tot+len(updated_kv)-len(existing_kv)
return "Added a total of {} kv pairs to {}/{} files ".format(nkv_tot,nimg_updated,nimg)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def getObjects(conn, scriptParams):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
"""
collect the object list from the script patameters
@param conn: Blitz Gateway connection wrapper
@param scriptParams: A map of the input parameters
"""
# we know scriptParams will have "Data_Type" and "IDs" since these
# parameters are not optional
dataType = scriptParams["Data_Type"]
ids = scriptParams["IDs"]
# dataType is 'Dataset' or 'Image' so we can use it directly in
# getObjects()
obs = conn.getObjects(dataType, ids) # generator of images or datasets
objects = list(obs)
return objects
if __name__ == "__main__":
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
dataTypes = [rstring('Dataset')] # only works on datasets
# Here we define the script name and description.
# Good practice to put url here to give users more guidance on how to run
# your script.
client = scripts.client(
'Key_Val_from_Description.py',
(" Adds key-value metadata pairs to images in a data set from "
" the description for a dataset or collections of datasets"
" k-v pairs taken from the dataset description"
" and by parsing the filename"
" Image IDs or by the Dataset IDs.\nSee"
" http://www.openmicroscopy.org/site/support/omero5.2/developers/"
"scripts/user-guide.html for the tutorial that uses this script."),
scripts.String(
"Data_Type", optional=False, grouping="1",
description="The data you want to work with.", values=dataTypes,
default="Dataset"),
scripts.List(
"IDs", optional=False, grouping="2",
description="List of Dataset IDs or Image IDs").ofType(rlong(0)),
version="5.3",
authors=["Christian Evenhuis", "MIF"],
institutions=["University of Technology Sydney"],
contact="christian.evenhuis@gmail.com"
)
try:
scriptParams = {}
for key in client.getInputKeys():
if client.getInput(key):
# unwrap rtypes to String, Integer etc
scriptParams[key] = client.getInput(key, unwrap=True)
print(scriptParams) # handy to have inputs in the std-out log
# wrap client to use the Blitz Gateway
conn = BlitzGateway(client_obj=client)
## do the editing...
datasets= getObjects(conn, scriptParams)
for ds in datasets:
print(ds.getName())
message = AddMapAnnotations( conn, 'Dataset', ds.getId() )
client.setOutput("Message", rstring(message))
## now handle the result, displaying message and returning image if
## appropriate
#if editedImgIds is None:
# message = "Script failed. See 'error' or 'info' for more details"
#else:
# if len(editedImgIds) == 1:
# # image-wrapper
# img = conn.getObject("Image", editedImgIds[0])
# message = "One Image edited: %s" % img.getName()
# # omero.model object
# omeroImage = img._obj
# # Insight will display 'View' link to image
# client.setOutput("Edited Image", robject(omeroImage))
# elif len(editedImgIds) > 1:
# message = "%s Images edited" % len(editedImgIds)
# else:
# message = ("No images edited. See 'error' or 'info' for more"
# " details")
# # Insight will display the 'Message' parameter
#client.setOutput("Message", rstring(message))
except:
pass
finally:
client.closeSession()