WIP: Add scripts for bulk annotation

omero/annotation_scripts/CONTRIBUTING.md

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+# OMERO User Scripts
+
+Please see our [User Scripts](https://www.openmicroscopy.org/info/scripts) page
+on how to use this repository.

omero/annotation_scripts/KeyVal_from_Filename.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:[email protected]">[email protected]</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:
+                ord_dict[k] = 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 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
+    template  = None 
+
+    for line in description:
+        # 1. See if this is a mode string
+        for key,value in modes.items():
+            match = re.search( "^#\s+{}".format(key),line.lower())
+            if( match is not None ):
+                mode = value
+                print("match",mode)
+                continue
+
+        if( mode == 'default' ):
+            pass
+
+        if( mode == 'global' ):
+            # split the line for the kay value pair
+            match = re.search("^\s*(\S+)\s*:\s*(\S+)",line)
+            if( match is not None ):
+                key = match.group(1)
+                val = match.group(2)
+                global_kv[key]=val
+                print("Found global match")
+                print(key,val)
+
+        if( mode == 'filename' ):
+             match = re.search( "^\s*template\s+(\S+)",line)
+             if( match is not None ):
+                 template = match.group(1)
+                 print("New template {}".format(template) )
+                           # 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))
+                 file_keys[i] = match.group(2)
+
+    print("Global k-v's")
+    for k,v in global_kv.items():
+        print( k,v)
+
+    # convert the template to a regexp
+                                 # not white space 
+                                 # or underscore
+                                 # or filesep
+    if( template is not None ):
+        print("What is the template?")
+        template="{}$".format(template)
+        print(template)
+        template= template.replace("*","([^\s_\/]+)")
+        template= template.replace("?","[^\s_\/]")
+        print(template)
+        regexp = re.compile(template)
+
+    # 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
+        map_ann.setNs(namespace)    
+        map_ann.setValue(  [  [k,v] for k,v in global_kv.items() ] )
+        map_ann.save()
+        dataset.linkAnnotation(map_ann)
+
+    # add the metadata to the images
+    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]
+                        updated_kv[key] = 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 = omero.constants.metadata.NSCLIENTMAPANNOTATION
+            map_ann.setNs(namespace)
+            # convert the ordered dict to a list of lists
+            map_ann.setValue([  [k,v] for k,v in updated_kv.items() ] )
+            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_FileName.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="[email protected]"
+
+    )
+
+    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))
+    finally:
+        client.closeSession()