From 37da1aa1d1f6143b33c3369a0cd6a345d59aeb92 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 21 Apr 2021 12:57:54 +0100
Subject: [PATCH 01/18] Add --ignore_datasets option to
 idr_get_map_annotations.py

---
 maintenance/scripts/delete_ROIs.py            |  2 +-
 .../scripts/idr_get_map_annotations.py        | 59 +++++++++++++------
 2 files changed, 41 insertions(+), 20 deletions(-)

diff --git a/maintenance/scripts/delete_ROIs.py b/maintenance/scripts/delete_ROIs.py
index bacb84ac..d58c845c 100644
--- a/maintenance/scripts/delete_ROIs.py
+++ b/maintenance/scripts/delete_ROIs.py
@@ -30,7 +30,7 @@ def run(name, password, dataset_name, dataset_id, host, port):
         conn.connect()
         roi_service = conn.getRoiService()
         datasets = []
-        if dataset_id >= 0:
+        if int(dataset_id) >= 0:
             datasets.append(conn.getObject("Dataset", dataset_id))
         else:
             datasets = conn.getObjects("Dataset",
diff --git a/maintenance/scripts/idr_get_map_annotations.py b/maintenance/scripts/idr_get_map_annotations.py
index 0d20b8ae..d3513826 100644
--- a/maintenance/scripts/idr_get_map_annotations.py
+++ b/maintenance/scripts/idr_get_map_annotations.py
@@ -48,13 +48,21 @@ def get_idr_datasets_as_dict(project_id):
     return by_name
 
 
-def get_idr_images_as_dict(dataset_id):
+def get_idr_images_as_dict(obj_id, dtype="Dataset"):
     """Get a dict of {name: {id: 1}} for Images in IDR Dataset."""
-    url = webclient_api_url + "images/?id=%s" % dataset_id
-    images = session.get(url).json()['images']
     by_name = {}
-    for i in images:
-        by_name[i['name']] = i
+    if dtype == "Dataset":
+        dataset_ids = [obj_id]
+    elif dtype == "Project":
+        datasets_url = webclient_api_url + "datasets/?id=%s" % obj_id
+        datasets = session.get(datasets_url).json()['datasets']
+        dataset_ids = [d['id'] for d in datasets]
+        print('dataset_ids', dataset_ids)
+    for dataset_id in dataset_ids:
+        url = webclient_api_url + "images/?id=%s" % dataset_id
+        images = session.get(url).json()['images']
+        for i in images:
+            by_name[i['name']] = i
     return by_name
 
 
@@ -73,19 +81,22 @@ def get_idr_wells_as_grid(plate_id):
     return session.get(url).json()['grid']
 
 
-def annotate_project(conn, local_id, idr_id):
+def annotate_project(conn, local_id, idr_id, ignore_datasets=False):
     project = conn.getObject("Project", local_id)
-    idr_datasets = get_idr_datasets_as_dict(idr_id)
+    idr_images = {}
+    if ignore_datasets:
+        idr_images = get_idr_images_as_dict(idr_id, "Project")
+    else:
+        idr_datasets = get_idr_datasets_as_dict(idr_id)
     for dataset in project.listChildren():
-
         print("\n\nDataset", dataset.id, dataset.name)
-        # Get IDR Dataset with same name:
-        idr_dataset = idr_datasets.get(dataset.name)
-        if idr_dataset is None:
-            print("    NO IDR Dataset found!")
-            continue
-
-        idr_images = get_idr_images_as_dict(idr_dataset['id'])
+        if not ignore_datasets:
+            # Get IDR Dataset with same name:
+            idr_dataset = idr_datasets.get(dataset.name)
+            if idr_dataset is None:
+                print("    NO IDR Dataset found!")
+                continue
+            idr_images = get_idr_images_as_dict(idr_dataset['id'])
         for image in dataset.listChildren():
 
             print("Image", image.id, image.name)
@@ -138,7 +149,16 @@ def annotate_plate(conn, plate, idr_plate_id):
         add_new_map_anns(conn, well, url)
 
 
-def run(username, password, idr_obj, local_obj, host, port):
+def run(args):
+
+    username = args.username
+    password = args.password
+    idr_obj = args.idr_obj
+    local_obj = args.local_obj
+    host = args.server
+    port = args.port
+    ignore_datasets = args.ignore_datasets
+    print('ignore_datasets', ignore_datasets)
 
     conn = BlitzGateway(username, password, host=host, port=port)
     try:
@@ -155,7 +175,7 @@ def run(username, password, idr_obj, local_obj, host, port):
             return
         local_id = local_obj.split(':')[1]
         if dtype == 'Project':
-            annotate_project(conn, local_id, idr_id)
+            annotate_project(conn, local_id, idr_id, ignore_datasets)
         elif dtype == 'Plate':
             plate = conn.getObject('Plate', local_id)
             annotate_plate(conn, plate, idr_id)
@@ -183,12 +203,13 @@ def main(args):
     parser.add_argument('password')
     parser.add_argument('idr_obj', help=obj_help),
     parser.add_argument('local_obj', help=obj_help)
+    parser.add_argument('--ignore_datasets', action='store_true',
+                        help="Can ignore Dataset names IF Images have unique names in Project")
     parser.add_argument('--server', default="workshop.openmicroscopy.org",
                         help="OMERO server hostname")
     parser.add_argument('--port', default=4064, help="OMERO server port")
     args = parser.parse_args(args)
-    run(args.username, args.password, args.idr_obj, args.local_obj,
-        args.server, args.port)
+    run(args)
 
 
 if __name__ == '__main__':

From dc0352ebd0ca1e3fea3ff73f223e5ca1995f8eba Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 21 Apr 2021 13:31:40 +0100
Subject: [PATCH 02/18] flake8 fix

---
 maintenance/scripts/idr_get_map_annotations.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/maintenance/scripts/idr_get_map_annotations.py b/maintenance/scripts/idr_get_map_annotations.py
index d3513826..a6ead8d4 100644
--- a/maintenance/scripts/idr_get_map_annotations.py
+++ b/maintenance/scripts/idr_get_map_annotations.py
@@ -203,8 +203,9 @@ def main(args):
     parser.add_argument('password')
     parser.add_argument('idr_obj', help=obj_help),
     parser.add_argument('local_obj', help=obj_help)
-    parser.add_argument('--ignore_datasets', action='store_true',
-                        help="Can ignore Dataset names IF Images have unique names in Project")
+    parser.add_argument(
+        '--ignore_datasets', action='store_true',
+        help="Can ignore Dataset names IF Images have unique names in Project")
     parser.add_argument('--server', default="workshop.openmicroscopy.org",
                         help="OMERO server hostname")
     parser.add_argument('--port', default=4064, help="OMERO server port")

From 8ddbc5ddb440f1038a7ace0eff2c98ca64f0851b Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 21 Apr 2021 14:03:14 +0100
Subject: [PATCH 03/18] Add --use_stain option to channel_names_from_maps.py

---
 .../scripts/channel_names_from_maps.py        | 24 ++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/maintenance/scripts/channel_names_from_maps.py b/maintenance/scripts/channel_names_from_maps.py
index 156d40af..c1e0863b 100644
--- a/maintenance/scripts/channel_names_from_maps.py
+++ b/maintenance/scripts/channel_names_from_maps.py
@@ -27,7 +27,16 @@
 MAP_KEY = "Channels"
 
 
-def run(username, password, project_id, host, port):
+def run(args):
+
+    username = args.username
+    password = args.password
+    project_id = args.project_id
+    host = args.server
+    port = args.port
+    use_stain = args.use_stain
+
+    token_index = 0 if use_stain else 1
 
     conn = BlitzGateway(username, password, host=host, port=port)
     try:
@@ -51,7 +60,12 @@ def run(username, password, project_id, host, port):
                 print("Channels", channels)
                 name_dict = {}
                 for c, ch_name in enumerate(channels):
-                    name_dict[c + 1] = ch_name.split(":")[1]
+                    tokens = ch_name.split(":")
+                    if len(tokens) > token_index:
+                        label = tokens[token_index]
+                    else:
+                        label = ch_name
+                    name_dict[c + 1] = label
                 conn.setChannelNames("Image", [image.id], name_dict,
                                      channelCount=None)
     except Exception as exc:
@@ -65,11 +79,15 @@ def main(args):
     parser.add_argument('username')
     parser.add_argument('password')
     parser.add_argument('project_id')
+    parser.add_argument(
+        '--use_stain', action='store_true',
+        help="""Map Ann Channels are in the form stain:label, e.g. DAPI:DNA.
+If use_stain, channels will be named with the stain instead of the label""")
     parser.add_argument('--server', default="workshop.openmicroscopy.org",
                         help="OMERO server hostname")
     parser.add_argument('--port', default=4064, help="OMERO server port")
     args = parser.parse_args(args)
-    run(args.username, args.password, args.project_id, args.server, args.port)
+    run(args)
 
 
 if __name__ == '__main__':

From a6bc39980cb1c550aefb3610d99441c4638faa39 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 21 Apr 2021 17:54:52 +0100
Subject: [PATCH 04/18] channel_names_from_maps.py has --add_map_anns option

---
 .../scripts/channel_names_from_maps.py        | 20 ++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/maintenance/scripts/channel_names_from_maps.py b/maintenance/scripts/channel_names_from_maps.py
index c1e0863b..fca2b559 100644
--- a/maintenance/scripts/channel_names_from_maps.py
+++ b/maintenance/scripts/channel_names_from_maps.py
@@ -20,12 +20,18 @@
 # Script uses map annotations on each Image to rename channels
 
 import argparse
-from omero.gateway import BlitzGateway
+from omero.gateway import BlitzGateway, MapAnnotationWrapper
 
 
 NAMESPACE = "openmicroscopy.org/omero/bulk_annotations"
 MAP_KEY = "Channels"
 
+def create_map_ann(conn, obj, key_value_data):
+    map_ann = MapAnnotationWrapper(conn)
+    map_ann.setValue(key_value_data)
+    map_ann.setNs('from.channels.keyvaluepair')
+    map_ann.save()
+    obj.linkAnnotation(map_ann)
 
 def run(args):
 
@@ -35,6 +41,7 @@ def run(args):
     host = args.server
     port = args.port
     use_stain = args.use_stain
+    add_map_anns = args.add_map_anns
 
     token_index = 0 if use_stain else 1
 
@@ -59,8 +66,13 @@ def run(args):
                 channels = values[0].split("; ")
                 print("Channels", channels)
                 name_dict = {}
+                key_value_pairs = []
                 for c, ch_name in enumerate(channels):
                     tokens = ch_name.split(":")
+                    if add_map_anns and len(tokens) > 1:
+                        key_value_pairs.extend(
+                            [["Ch%s_Stain" % c, tokens[0]], ["Ch%s_Label" % c, tokens[1]]]
+                        )
                     if len(tokens) > token_index:
                         label = tokens[token_index]
                     else:
@@ -68,6 +80,8 @@ def run(args):
                     name_dict[c + 1] = label
                 conn.setChannelNames("Image", [image.id], name_dict,
                                      channelCount=None)
+                if len(key_value_pairs) > 0:
+                    create_map_ann(conn, image, key_value_pairs)
     except Exception as exc:
         print("Error while changing names: %s" % str(exc))
     finally:
@@ -83,6 +97,10 @@ def main(args):
         '--use_stain', action='store_true',
         help="""Map Ann Channels are in the form stain:label, e.g. DAPI:DNA.
 If use_stain, channels will be named with the stain instead of the label""")
+    parser.add_argument(
+        '--add_map_anns', action='store_true',
+        help="""Create new Map Anns of the form
+Ch1_Stain:DAPI, Ch1_Label:DNA etc using the Channels Key-Value Pair""")
     parser.add_argument('--server', default="workshop.openmicroscopy.org",
                         help="OMERO server hostname")
     parser.add_argument('--port', default=4064, help="OMERO server port")

From 1ba26e1ec3898e0caeff529ef3ef334202b171e6 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 21 Apr 2021 18:08:02 +0100
Subject: [PATCH 05/18] Flake8 fix

---
 maintenance/scripts/channel_names_from_maps.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/maintenance/scripts/channel_names_from_maps.py b/maintenance/scripts/channel_names_from_maps.py
index fca2b559..0ed5c70f 100644
--- a/maintenance/scripts/channel_names_from_maps.py
+++ b/maintenance/scripts/channel_names_from_maps.py
@@ -26,6 +26,7 @@
 NAMESPACE = "openmicroscopy.org/omero/bulk_annotations"
 MAP_KEY = "Channels"
 
+
 def create_map_ann(conn, obj, key_value_data):
     map_ann = MapAnnotationWrapper(conn)
     map_ann.setValue(key_value_data)
@@ -33,8 +34,8 @@ def create_map_ann(conn, obj, key_value_data):
     map_ann.save()
     obj.linkAnnotation(map_ann)
 
-def run(args):
 
+def run(args):
     username = args.username
     password = args.password
     project_id = args.project_id
@@ -71,7 +72,8 @@ def run(args):
                     tokens = ch_name.split(":")
                     if add_map_anns and len(tokens) > 1:
                         key_value_pairs.extend(
-                            [["Ch%s_Stain" % c, tokens[0]], ["Ch%s_Label" % c, tokens[1]]]
+                            [["Ch%s_Stain" % c, tokens[0]],
+                             ["Ch%s_Label" % c, tokens[1]]]
                         )
                     if len(tokens) > token_index:
                         label = tokens[token_index]

From 46acd053a4c88fe6f9019a58ed923a0ae3200a69 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Mon, 26 Apr 2021 09:51:57 +0100
Subject: [PATCH 06/18] calibrate_images.py target supports Project:ID

---
 maintenance/scripts/calibrate_images.py | 112 ++++++++++++++++++------
 1 file changed, 86 insertions(+), 26 deletions(-)

diff --git a/maintenance/scripts/calibrate_images.py b/maintenance/scripts/calibrate_images.py
index 5654a6c2..7a7ca574 100644
--- a/maintenance/scripts/calibrate_images.py
+++ b/maintenance/scripts/calibrate_images.py
@@ -33,9 +33,50 @@
 from omero.model.enums import UnitsLength
 
 
-def run(password, target, host, port):
-
-    for i in range(1, 51):
+def setPixelSize(conn, image, value, unit):
+    print('Image', image.id, value)
+    value_z = None
+    if 'x' in value:
+        value_xy = float(value.split('x')[0])
+        value_z = float(value.split('x')[1])
+    else:
+        value_xy = float(value)
+    xy = omero.model.LengthI(value_xy, getattr(UnitsLength, unit))
+    p = image.getPrimaryPixels()._obj
+    p.setPhysicalSizeX(xy)
+    p.setPhysicalSizeY(xy)
+    if value_z is not None:
+        z = omero.model.LengthI(value_z, getattr(UnitsLength, unit))
+        p.setPhysicalSizeZ(z)
+    conn.getUpdateService().saveObject(p)
+
+
+def set_by_target_id(password, username, target, host, port, value, unit):
+
+    conn = BlitzGateway(username, password, host=host, port=port)
+    conn.connect()
+    target_type = target.split(':')[0]
+    target_id = int(target.split(':')[1])
+    if target_type not in ['Project', 'Dataset', 'Image']:
+        print("Target must be Project:ID, Dataset:ID or Image:ID")
+        return
+    images = []
+    if target_type == "Project":
+        for dataset in conn.getObject('Project', target_id).listChildren():
+            images.extend((list(dataset.listChildren())))
+    elif target_type == "Dataset":
+        images = list(conn.getObject('Dataset', target_id).listChildren())
+    elif target_type == "Image":
+        images = [conn.getObject("Image", target_id)]
+    print('images', images)
+
+    for image in images:
+        setPixelSize(conn, image, value, unit)
+
+
+def set_for_users_by_dataset_name(password, target, host, port, value, unit):
+
+    for i in range(1, 2):
 
         username = "user-%s" % i
         print(username)
@@ -56,42 +97,61 @@ def run(password, target, host, port):
 
             dataset_obj = dataset[0]
             datasetId = dataset[0].getId().getValue()
-
             print('dataset', datasetId)
-            params2 = omero.sys.ParametersI()
-            params2.addId(dataset_obj.getId())
-            query = "select l.child.id from DatasetImageLink \
-                     l where l.parent.id = :id"
-            images = service.projection(query, params2, conn.SERVICE_OPTS)
-            values = []
-            for k in range(0, len(images)):
-
-                image_id = images[k][0].getValue()
-                image = conn.getObject("Image", image_id)
-
-                u = omero.model.LengthI(0.33, UnitsLength.MICROMETER)
-                p = image.getPrimaryPixels()._obj
-                p.setPhysicalSizeX(u)
-                p.setPhysicalSizeY(u)
-                values.append(p)
-
-            if len(images) > 0:
-                conn.getUpdateService().saveArray(values)
+            for image in conn.getObject("Dataset", datasetId).listChildren():
+                setPixelSize(conn, image, value, unit)
         except Exception as exc:
             print("Error during calibration: %s" % str(exc))
         finally:
             conn.close()
 
+def run(args):
+    password = args.password
+    target = args.target
+    value = args.value
+    unit = args.unit
+    host = args.server
+    port = args.port
+
+    # Handle target is e.g. "Project:1"
+    if ':' in target:
+        try:
+            target_id = int(target.split(':')[1])
+            set_by_target_id(password, args.user, target, host, port, value, unit)
+            return
+        except ValueError:
+            print("Not valid Project or Dataset ID")
+
+    # Assume that target was a Dataset Name
+    set_for_users_by_dataset_name(password, target, host, port, value, unit)
 
 def main(args):
+    """
+    The script sets Pixels Sizes in 2 use-cases. 
+    Each needs a pixel size 'value' eg. 0.85 for X and Y or '0.85x0.2' for XY and Z
+    Units are optional. Default is "MICROMETER".
+
+    1) For many users 'user-1...user-50' etc with a NAMED Dataset
+    $ calibrate_images.py [password] [dataset_name] [value] --server [server]
+
+    2) For a single user, where the target is Project:ID or Dataset:ID
+    $ calibrate_images.py [password] [target] [value] --user [username] --server [server]
+    """
     parser = argparse.ArgumentParser()
     parser.add_argument('password')
-    parser.add_argument('target')
-    parser.add_argument('--server', default="workshop.openmicroscopy.org",
+    parser.add_argument(
+        'target',
+        help="Dataset name (for many users) or target Project/Dataset/Image:ID")
+    parser.add_argument('value', help="Pixel size value")
+    parser.add_argument('--unit', default="MICROMETER",
+        help="Unit from omero.")
+    parser.add_argument('--user', help="Username ONLY if single user")
+    parser.add_argument('--server', default="localhost",
                         help="OMERO server hostname")
     parser.add_argument('--port', default=4064, help="OMERO server port")
     args = parser.parse_args(args)
-    run(args.password, args.target, args.server, args.port)
+
+    run(args)
 
 
 if __name__ == '__main__':

From c321d2e87b96996a63446b1de8c617c598bfc12d Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 11 May 2021 14:45:55 +0100
Subject: [PATCH 07/18] simple_frap_with_figure.py labels in milliseconds

---
 practical/python/server/simple_frap_with_figure.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/practical/python/server/simple_frap_with_figure.py b/practical/python/server/simple_frap_with_figure.py
index 8d24c30a..eb295550 100644
--- a/practical/python/server/simple_frap_with_figure.py
+++ b/practical/python/server/simple_frap_with_figure.py
@@ -208,8 +208,8 @@ def create_omero_figure(conn, images, plots):
             panel_x = (col * (panel_height + spacing)) + margin
             j = get_panel_json(image, panel_x, panel_y,
                                panel_width, panel_height, the_t)
-            # Add timestamp in 'secs' to top-left of each movie frame
-            j['labels'] = [{"time": "secs",
+            # Add timestamp in 'milliseconds' to top-left of each movie frame
+            j['labels'] = [{"time": "milliseconds",
                             "size": "12",
                             "position": "topleft",
                             "color": "FFFFFF"}]

From b90cd4bb4cd445e7977e17a4c3532cda8f49f13f Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 26 May 2021 16:26:31 +0100
Subject: [PATCH 08/18] Add figure_image_table_shape_heatmap.js

---
 .../figure_image_table_shape_heatmap.js       | 60 +++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 practical/javascript/figure_image_table_shape_heatmap.js

diff --git a/practical/javascript/figure_image_table_shape_heatmap.js b/practical/javascript/figure_image_table_shape_heatmap.js
new file mode 100644
index 00000000..2ef94f69
--- /dev/null
+++ b/practical/javascript/figure_image_table_shape_heatmap.js
@@ -0,0 +1,60 @@
+
+//
+// Copyright (C) 2021 University of Dundee & Open Microscopy Environment.
+// All rights reserved.
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License as
+// published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
+//
+// You should have received a copy of the GNU Affero General Public License
+// along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+// Using the browser devtools to manipulate OMERO.figure is an experimental
+// feature for developers.
+// N.B.: Never paste untrusted code into your browser console.
+//
+// This script requires an OMERO.table linked to the Image
+// with a 'Shape' column and another numerical named column (edit below).
+// Select panel with Shapes added from OMERO (shape.id should be in the table).
+// This colors each Shape according to a heatmap for the named column.
+
+async function shapeData(panel) {
+    const shapeIds = panel.get("shapes").map(s => s.id).filter(id => id > 0);
+    console.log('shapeIds', shapeIds);
+    let vals_by_shape = {};
+    for (let i = 0; i < shapeIds.length; i++) {
+        // Load one at a time - more reliable
+        let url = `/webgateway/table/Image/${panel.get('imageId')}/query/?query=Shape-${shapeIds[i]}`;
+        let r = await fetch(url).then(rsp => rsp.json());
+        let colIndex = r.data?.columns?.indexOf("Centroids_RAW_X");
+        let shapeIndex = r.data?.columns?.indexOf("Shape");
+        if (colIndex && shapeIndex && r.data?.rows.length > 0) {
+            console.log("Value", r.data.rows[0][colIndex]);
+            vals_by_shape[r.data.rows[0][shapeIndex]] = r.data.rows[0][colIndex];
+        }
+    };
+    // Once all loaded, we can calculate range and assign colours to shapes
+    const values = Object.values(vals_by_shape);
+    let minVal = Math.min(...values);
+    let valRange = Math.max(...values) - minVal;
+    console.log('min, range', minVal, valRange);
+    const new_shapes = panel.get("shapes").map(shape => {
+        // hide any shapes we don't have data for
+        if (!vals_by_shape[shape.id]) return { ...shape, strokeWidth: 0.01 };
+        let value = (vals_by_shape[shape.id] - minVal) / valRange;
+        let red = parseInt(value * 255).toString(16);
+        let blue = (255 - parseInt(value * 255)).toString(16);
+        red = red.length == 1 ? `0` + red : red;
+        blue = blue.length == 1 ? `0` + blue : blue;
+        return { ...shape, strokeColor: `#${red}00${blue}`, strokeWidth: 5 }
+    });
+    panel.set('shapes', new_shapes);
+}
+figureModel.getSelected().forEach(shapeData);

From 95946fb178bd7833237ca0411671df8a63fc215c Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 26 May 2021 16:26:57 +0100
Subject: [PATCH 09/18] Add preparation/idr0079-data-prep.md

---
 maintenance/preparation/idr0079-data-prep.md | 103 +++++++++++++++++++
 1 file changed, 103 insertions(+)
 create mode 100644 maintenance/preparation/idr0079-data-prep.md

diff --git a/maintenance/preparation/idr0079-data-prep.md b/maintenance/preparation/idr0079-data-prep.md
new file mode 100644
index 00000000..2e131766
--- /dev/null
+++ b/maintenance/preparation/idr0079-data-prep.md
@@ -0,0 +1,103 @@
+
+Workshop data preparation (idr0079)
+===================================
+
+This document details the steps to prepare data from idr0079 for use in an OMERO.parade
+and OMERO.figure workshop. 
+
+
+IDR data import
+===============
+
+For OME team, steps for in-place import of IDR data can be found at
+https://docs.google.com/document/d/18cLSvUKVn8jEp7KSW7e48NvuxHT_mp3tyh98loTTOYY/edit
+
+For other users, you will need to have Docker installed.
+This container uses Aspera to download the data from EBI:
+
+	$ docker run --rm -v /tmp:/data imagedata/download idr0021 . /data/
+
+Clone https://github.com/IDR/idr0079-hartmann-lateralline and edit
+```experimentA/idr0079-experimentA-filePaths.tsv```
+to point ALL paths at the location of the data downloaded above.
+
+If you don't want to use in-place import, comment out this line in
+```experimentA/idr0079-experimentA-bulk.yml```:
+
+	transfer: "ln_s"
+
+
+Do the bulk import:
+
+	$ cd experimentA/
+	$ omero import --bulk idr0079-experimentA-bulk.yml
+
+
+Add Map Annotations from IDR
+============================
+
+Use the script [idr_get_map_annotations.py](../scripts/idr_get_map_annotations.py) with the ID of
+the 'idr0079-hartmann-lateralline/experimentA' Project created above and the corresponding
+Project on IDR (1102):
+
+	$ python idr_get_map_annotations.py username password Project:1102 Project:1301 --server localhost
+
+This will get map annotations from all Images in `idr0079-hartmann-lateralline/experimentA` and
+create identical map annotations on the corresponding Images.
+
+
+Rename Channels from Map Annotations
+====================================
+
+We can now use the map annotations to rename channels on all images.
+Run the [channel_names_from_maps.py](../scripts/channel_names_from_maps.py)
+script on the local data, using the local Project ID.
+We are using the `stain` to name channels, e.g. `NLStdTomato`, and also adding
+map annotations for inidividual channels to use for label creation in OMERO.figure:
+
+    $ python channel_names_from_maps.py username password 1301 --server localhost --use_stain --add_map_anns
+
+
+Manual Annotations and Rendering Settings
+=========================================
+
+Add 5* rating to 1 image each from membranes_actin, membranes_cisgolgi, membranes_nuclei, membranes_recendo.
+
+Set rendering settings: Channel-1: Green, Channel-2: Red. Maybe adjust levels too.
+
+Set Pixel Sizes
+==========================================
+
+See the commands used for IDR at [idr0079_voxel_sizes.sh]
+(https://github.com/will-moore/idr0079-hartmann-lateralline/blob/voxel_sizes/scripts/idr0079_voxel_sizes.sh)
+and run these commands on the local server, using the appropriate Dataset IDs.
+
+Copy Masks to Polygons
+======================
+
+The idr0079 images in IDR have Masks, but we want to use Polygons in OMERO.figure.
+Use the [copy_masks_2_polygons.py](../scripts/copy_masks_2_polygons.py) script to
+convert. NB: requires `skimage`. We want to copy to each of the 5-star rated
+images above, in turn, from the ID of the corresponding Image to the local Image ID
+
+    # login to IDR
+    $ omero login
+    # copy to local server
+    $ python copy_masks_2_polygons.py username password server FROM_IMAGE_ID TO_IMAGE_ID
+
+Create OMERO.tables
+===================
+
+We use the tsv files in https://github.com/IDR/idr0079-hartmann-lateralline to create
+an OMERO.table on the Project, with one row per Image, summarising the stats for all the
+ROIs in that Image. This uses [csv_to_table_on_project.py](https://github.com/will-moore/idr0079-hartmann-lateralline/blob/csv_to_tables_scripts/scripts/csv_to_table_on_project.py)
+
+Clone the github repo, then:
+
+    $ cd idr0079-hartmann-lateralline
+    $ python scripts/csv_to_table_on_project.py
+
+We then create an OMERO.table on each Image that has ROIs added above:
+Use the optional `--name NAME` to run on a single named Image:
+
+    $ python scripts/csv_to_roi_table

From ffba0da9cd0cc353a7d15a9167b9c463f149e59f Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 26 May 2021 16:34:46 +0100
Subject: [PATCH 10/18] Add copy_masks_2_polygons.py

---
 maintenance/scripts/copy_masks_2_polygons.py | 176 +++++++++++++++++++
 1 file changed, 176 insertions(+)
 create mode 100644 maintenance/scripts/copy_masks_2_polygons.py

diff --git a/maintenance/scripts/copy_masks_2_polygons.py b/maintenance/scripts/copy_masks_2_polygons.py
new file mode 100644
index 00000000..9ec67124
--- /dev/null
+++ b/maintenance/scripts/copy_masks_2_polygons.py
@@ -0,0 +1,176 @@
+
+import omero
+from omero.gateway import BlitzGateway
+from omero.rtypes import rint, rstring
+
+from skimage import morphology
+from skimage import measure
+
+import argparse
+import sys
+import numpy as np
+
+import omero
+import omero.clients
+from omero.rtypes import unwrap, rint, rstring
+from omero.cli import cli_login
+from omero.api import RoiOptions
+from omero.gateway import BlitzGateway
+
+
+def mask_to_binim_yx(mask):
+    """
+    # code from omero-cli-zarr
+    :param mask MaskI: An OMERO mask
+
+    :return: tuple of
+            - Binary mask
+            - (T, C, Z, Y, X, w, h) tuple of mask settings (T, C, Z may be
+            None)
+    """
+
+    t = unwrap(mask.theT)
+    c = unwrap(mask.theC)
+    z = unwrap(mask.theZ)
+
+    x = int(mask.x.val)
+    y = int(mask.y.val)
+    w = int(mask.width.val)
+    h = int(mask.height.val)
+
+    mask_packed = mask.getBytes()
+    # convert bytearray into something we can use
+    intarray = np.fromstring(mask_packed, dtype=np.uint8)
+    binarray = np.unpackbits(intarray)   #.astype(self.dtype)
+    # truncate and reshape
+    binarray = np.reshape(binarray[: (w * h)], (h, w))
+
+    return binarray, (t, c, z, y, x, h, w)
+
+
+def rgba_to_int(red, green, blue, alpha=255):
+    """ Return the color as an Integer in RGBA encoding """
+    r = red << 24
+    g = green << 16
+    b = blue << 8
+    a = alpha
+    rgba_int = r+g+b+a
+    if (rgba_int > (2**31-1)):       # convert to signed 32-bit int
+        rgba_int = rgba_int - 2**32
+    return rgba_int
+
+
+def get_longest_contour(contours):
+    contour = contours[0]
+    for c in contours:
+        if len(c) > len(contour):
+            contour = c
+    return c
+
+
+def add_polygon(roi, contour, x_offset=0, y_offset=0, z=None, t=None):
+    """ points is 2D list of [[x, y], [x, y]...]"""
+
+    stride = 4
+    coords = []
+    # points in contour are adjacent pixels, which is too verbose
+    # take every nth point
+    for count, xy in enumerate(contour):
+        if count%stride == 0:
+            coords.append(xy)
+    if len(coords) < 2:
+        return
+    points = ["%s,%s" % (xy[1] + x_offset, xy[0] + y_offset) for xy in coords]
+    points = ", ".join(points)
+
+    polygon = omero.model.PolygonI()
+    if z is not None:
+        polygon.theZ = rint(z)
+    if t is not None:
+        polygon.theT = rint(t)
+    polygon.strokeColor = rint(rgba_to_int(255, 255, 255))
+    # points = "10,20, 50,150, 200,200, 250,75"
+    polygon.points = rstring(points)
+    roi.addShape(polygon)
+
+
+def main(argv):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('username2', help='Target server Username')
+    parser.add_argument('password2', help='Target server Password')
+    parser.add_argument('server2', help='Target server')
+    parser.add_argument('imageid', type=int, help=(
+        'Copy ROIs FROM this image'))
+    parser.add_argument('imageid2', type=int, help=(
+        'Copy ROIs TO this image'))
+    args = parser.parse_args(argv)
+
+    to_image_id = args.imageid2
+
+    PAGE_SIZE = 50
+
+    with cli_login() as cli:
+        conn = BlitzGateway(client_obj=cli._client)
+        conn2 = BlitzGateway(args.username2, args.password2,
+                             port=4064, host=args.server2)
+        conn2.connect()
+
+        roi_service = conn.getRoiService()
+        update_service = conn2.getUpdateService()
+
+        opts = RoiOptions()
+        offset = 0
+        opts.offset = rint(offset)
+        opts.limit = rint(PAGE_SIZE)
+
+        conn.SERVICE_OPTS.setOmeroGroup(-1)
+        image = conn.getObject('Image', args.imageid)
+        size_x = image.getSizeX()
+        size_y = image.getSizeY()
+        print(image.name)
+
+        # NB: we repeat this query below for each 'page' of ROIs
+        result = roi_service.findByImage(args.imageid, opts, conn.SERVICE_OPTS)
+
+        while len(result.rois) > 0:
+            print("offset", offset)
+            print("Found ROIs:", len(result.rois))
+            for roi in result.rois:
+
+                new_roi = omero.model.RoiI()
+                new_roi.setImage(omero.model.ImageI(to_image_id, False))
+                shapes_added = False
+
+                for shape in roi.copyShapes():
+
+                    if not isinstance(shape, omero.model.MaskI):
+                        continue
+                    # assume shape is a Mask
+                    np_mask, dims = mask_to_binim_yx(shape)
+                    print('shape', np_mask.shape)
+                    t, c, z, y, x, h, w = dims
+                    print('dims', dims)
+                    image = np.zeros((size_y, size_x))
+                    image[y:y+h, x:x+w] = np_mask
+                    contours = measure.find_contours(image, 0.5)
+                    print('Found contours:', len(contours))
+                    if len(contours) > 0:
+                        contour = get_longest_contour(contours)
+                        # Only add 1 Polygon per Mask Shape.
+                        # First is usually the longest
+                        add_polygon(new_roi, contour, 0, 0, z, t)
+                    shapes_added = True
+
+                if shapes_added:
+                    update_service.saveObject(new_roi)
+
+            offset += PAGE_SIZE
+            opts.offset = rint(offset)
+            result = roi_service.findByImage(args.imageid, opts, conn.SERVICE_OPTS)
+
+        conn2.close()
+
+if __name__ == '__main__':
+    # First, login to source OMERO $ omero login
+    # Copy to target server: $ python copy_masks_2_polygons.py username password server FROM_IMAGE TO_IMAGE
+    main(sys.argv[1:])

From 3a851474dbc60f08101ce3ffbfe4ae91879770b7 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Thu, 27 May 2021 15:01:58 +0100
Subject: [PATCH 11/18] flake8 fixes

---
 maintenance/scripts/calibrate_images.py      | 21 +++++++++++---------
 maintenance/scripts/copy_masks_2_polygons.py | 18 ++++++++---------
 2 files changed, 20 insertions(+), 19 deletions(-)

diff --git a/maintenance/scripts/calibrate_images.py b/maintenance/scripts/calibrate_images.py
index 7a7ca574..453d2a34 100644
--- a/maintenance/scripts/calibrate_images.py
+++ b/maintenance/scripts/calibrate_images.py
@@ -95,7 +95,6 @@ def set_for_users_by_dataset_name(password, target, host, port, value, unit):
                 print("No dataset with name %s found" % target)
                 continue
 
-            dataset_obj = dataset[0]
             datasetId = dataset[0].getId().getValue()
             print('dataset', datasetId)
             for image in conn.getObject("Dataset", datasetId).listChildren():
@@ -105,6 +104,7 @@ def set_for_users_by_dataset_name(password, target, host, port, value, unit):
         finally:
             conn.close()
 
+
 def run(args):
     password = args.password
     target = args.target
@@ -116,8 +116,9 @@ def run(args):
     # Handle target is e.g. "Project:1"
     if ':' in target:
         try:
-            target_id = int(target.split(':')[1])
-            set_by_target_id(password, args.user, target, host, port, value, unit)
+            int(target.split(':')[1])
+            set_by_target_id(password, args.user, target, host, port,
+                             value, unit)
             return
         except ValueError:
             print("Not valid Project or Dataset ID")
@@ -125,26 +126,28 @@ def run(args):
     # Assume that target was a Dataset Name
     set_for_users_by_dataset_name(password, target, host, port, value, unit)
 
+
 def main(args):
     """
-    The script sets Pixels Sizes in 2 use-cases. 
-    Each needs a pixel size 'value' eg. 0.85 for X and Y or '0.85x0.2' for XY and Z
+    The script sets Pixels Sizes in 2 use-cases.
+    Each needs a pixel size 'value' eg. 0.85 for X and Y or
+    '0.85x0.2' for XY and Z.
     Units are optional. Default is "MICROMETER".
 
     1) For many users 'user-1...user-50' etc with a NAMED Dataset
-    $ calibrate_images.py [password] [dataset_name] [value] --server [server]
+    $ calibrate_images.py [password] [dataset_name] [value] --server [host]
 
     2) For a single user, where the target is Project:ID or Dataset:ID
-    $ calibrate_images.py [password] [target] [value] --user [username] --server [server]
+    calibrate_images.py [pass] [target] [value] --user [name] --server [host]
     """
     parser = argparse.ArgumentParser()
     parser.add_argument('password')
     parser.add_argument(
         'target',
-        help="Dataset name (for many users) or target Project/Dataset/Image:ID")
+        help="Dataset name (for many users) or Project/Dataset/Image:ID")
     parser.add_argument('value', help="Pixel size value")
     parser.add_argument('--unit', default="MICROMETER",
-        help="Unit from omero.")
+                        help="Unit from omero.")
     parser.add_argument('--user', help="Username ONLY if single user")
     parser.add_argument('--server', default="localhost",
                         help="OMERO server hostname")
diff --git a/maintenance/scripts/copy_masks_2_polygons.py b/maintenance/scripts/copy_masks_2_polygons.py
index 9ec67124..c308d1a6 100644
--- a/maintenance/scripts/copy_masks_2_polygons.py
+++ b/maintenance/scripts/copy_masks_2_polygons.py
@@ -1,9 +1,4 @@
 
-import omero
-from omero.gateway import BlitzGateway
-from omero.rtypes import rint, rstring
-
-from skimage import morphology
 from skimage import measure
 
 import argparse
@@ -12,10 +7,10 @@
 
 import omero
 import omero.clients
+from omero.gateway import BlitzGateway
 from omero.rtypes import unwrap, rint, rstring
 from omero.cli import cli_login
 from omero.api import RoiOptions
-from omero.gateway import BlitzGateway
 
 
 def mask_to_binim_yx(mask):
@@ -41,7 +36,7 @@ def mask_to_binim_yx(mask):
     mask_packed = mask.getBytes()
     # convert bytearray into something we can use
     intarray = np.fromstring(mask_packed, dtype=np.uint8)
-    binarray = np.unpackbits(intarray)   #.astype(self.dtype)
+    binarray = np.unpackbits(intarray)
     # truncate and reshape
     binarray = np.reshape(binarray[: (w * h)], (h, w))
 
@@ -76,7 +71,7 @@ def add_polygon(roi, contour, x_offset=0, y_offset=0, z=None, t=None):
     # points in contour are adjacent pixels, which is too verbose
     # take every nth point
     for count, xy in enumerate(contour):
-        if count%stride == 0:
+        if count % stride == 0:
             coords.append(xy)
     if len(coords) < 2:
         return
@@ -166,11 +161,14 @@ def main(argv):
 
             offset += PAGE_SIZE
             opts.offset = rint(offset)
-            result = roi_service.findByImage(args.imageid, opts, conn.SERVICE_OPTS)
+            result = roi_service.findByImage(args.imageid, opts,
+                                             conn.SERVICE_OPTS)
 
         conn2.close()
 
+
 if __name__ == '__main__':
     # First, login to source OMERO $ omero login
-    # Copy to target server: $ python copy_masks_2_polygons.py username password server FROM_IMAGE TO_IMAGE
+    # Copy to target server, with Image IDs
+    # $ python copy_masks_2_polygons.py user pass server FROM_IID TO_IID
     main(sys.argv[1:])

From b42bbfc3153ce97e3b9eb3ac6bd9b1fe1778dbf3 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Thu, 27 May 2021 15:05:41 +0100
Subject: [PATCH 12/18] Typo fixes

---
 maintenance/preparation/idr0079-data-prep.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/maintenance/preparation/idr0079-data-prep.md b/maintenance/preparation/idr0079-data-prep.md
index 2e131766..35a0832a 100644
--- a/maintenance/preparation/idr0079-data-prep.md
+++ b/maintenance/preparation/idr0079-data-prep.md
@@ -15,7 +15,7 @@ https://docs.google.com/document/d/18cLSvUKVn8jEp7KSW7e48NvuxHT_mp3tyh98loTTOYY/
 For other users, you will need to have Docker installed.
 This container uses Aspera to download the data from EBI:
 
-	$ docker run --rm -v /tmp:/data imagedata/download idr0021 . /data/
+	$ docker run --rm -v /tmp:/data imagedata/download idr0079 . /data/
 
 Clone https://github.com/IDR/idr0079-hartmann-lateralline and edit
 ```experimentA/idr0079-experimentA-filePaths.tsv```
@@ -53,7 +53,7 @@ We can now use the map annotations to rename channels on all images.
 Run the [channel_names_from_maps.py](../scripts/channel_names_from_maps.py)
 script on the local data, using the local Project ID.
 We are using the `stain` to name channels, e.g. `NLStdTomato`, and also adding
-map annotations for inidividual channels to use for label creation in OMERO.figure:
+map annotations for individual channels to use for label creation in OMERO.figure:
 
     $ python channel_names_from_maps.py username password 1301 --server localhost --use_stain --add_map_anns
 
@@ -101,3 +101,4 @@ We then create an OMERO.table on each Image that has ROIs added above:
 Use the optional `--name NAME` to run on a single named Image:
 
     $ python scripts/csv_to_roi_table
+

From 33b8386f590c28d5d68594e77d9c85dbcc29bcc1 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Mon, 21 Jun 2021 17:59:37 +0100
Subject: [PATCH 13/18] copy_masks_2_polygons.py handles Dataset or Image

---
 maintenance/scripts/copy_masks_2_polygons.py | 161 ++++++++++++-------
 1 file changed, 99 insertions(+), 62 deletions(-)

diff --git a/maintenance/scripts/copy_masks_2_polygons.py b/maintenance/scripts/copy_masks_2_polygons.py
index c308d1a6..92c20b81 100644
--- a/maintenance/scripts/copy_masks_2_polygons.py
+++ b/maintenance/scripts/copy_masks_2_polygons.py
@@ -12,6 +12,7 @@
 from omero.cli import cli_login
 from omero.api import RoiOptions
 
+PAGE_SIZE = 10
 
 def mask_to_binim_yx(mask):
     """
@@ -63,6 +64,13 @@ def get_longest_contour(contours):
     return c
 
 
+def image_ids_by_name(dataset):
+    ids_by_name = {}
+    for image in dataset.listChildren():
+        ids_by_name[image.name] = image.id
+    return ids_by_name
+
+
 def add_polygon(roi, contour, x_offset=0, y_offset=0, z=None, t=None):
     """ points is 2D list of [[x, y], [x, y]...]"""
 
@@ -89,86 +97,115 @@ def add_polygon(roi, contour, x_offset=0, y_offset=0, z=None, t=None):
     roi.addShape(polygon)
 
 
+def process_image(conn, conn2, image, to_image_id):
+    roi_service = conn.getRoiService()
+    update_service = conn2.getUpdateService()
+
+    print("Processing...", image.name, image.id)
+
+    old = conn2.getRoiService().findByImage(to_image_id, None, conn2.SERVICE_OPTS)
+    if len(old.rois) > 0:
+        print("Image", to_image_id, "already has ROIs. Ignoring...")
+        return
+
+    opts = RoiOptions()
+    offset = 0
+    opts.offset = rint(offset)
+    opts.limit = rint(PAGE_SIZE)
+
+    size_x = image.getSizeX()
+    size_y = image.getSizeY()
+
+    # NB: we repeat this query below for each 'page' of ROIs
+    result = roi_service.findByImage(image.id, opts, conn.SERVICE_OPTS)
+
+    while len(result.rois) > 0:
+        print("offset", offset)
+        print("Found ROIs:", len(result.rois))
+        for roi in result.rois:
+
+            new_roi = omero.model.RoiI()
+            new_roi.setImage(omero.model.ImageI(to_image_id, False))
+            shapes_added = False
+
+            for shape in roi.copyShapes():
+
+                if not isinstance(shape, omero.model.MaskI):
+                    continue
+                # assume shape is a Mask
+                np_mask, dims = mask_to_binim_yx(shape)
+                t, c, z, y, x, h, w = dims
+                plane = np.zeros((size_y, size_x))
+                plane[y:y+h, x:x+w] = np_mask
+                contours = measure.find_contours(plane, 0.5)
+                print('Found contours:', len(contours))
+                if len(contours) > 0:
+                    contour = get_longest_contour(contours)
+                    # Only add 1 Polygon per Mask Shape.
+                    # First is usually the longest
+                    add_polygon(new_roi, contour, 0, 0, z, t)
+                shapes_added = True
+
+            if shapes_added:
+                update_service.saveObject(new_roi)
+
+        offset += PAGE_SIZE
+        opts.offset = rint(offset)
+        result = roi_service.findByImage(image.id, opts, conn.SERVICE_OPTS)
+
+
 def main(argv):
     parser = argparse.ArgumentParser()
     parser.add_argument('username2', help='Target server Username')
     parser.add_argument('password2', help='Target server Password')
     parser.add_argument('server2', help='Target server')
-    parser.add_argument('imageid', type=int, help=(
-        'Copy ROIs FROM this image'))
-    parser.add_argument('imageid2', type=int, help=(
-        'Copy ROIs TO this image'))
+    parser.add_argument('source', help=(
+        'Copy ROIs FROM this: Image:ID or Dataset:ID'))
+    parser.add_argument('target', help=(
+        'Copy ROIs TO this: Image:ID or Dataset:ID'))
     args = parser.parse_args(argv)
 
-    to_image_id = args.imageid2
-
-    PAGE_SIZE = 50
 
     with cli_login() as cli:
         conn = BlitzGateway(client_obj=cli._client)
+        conn.SERVICE_OPTS.setOmeroGroup(-1)
+
         conn2 = BlitzGateway(args.username2, args.password2,
                              port=4064, host=args.server2)
         conn2.connect()
 
-        roi_service = conn.getRoiService()
-        update_service = conn2.getUpdateService()
-
-        opts = RoiOptions()
-        offset = 0
-        opts.offset = rint(offset)
-        opts.limit = rint(PAGE_SIZE)
-
-        conn.SERVICE_OPTS.setOmeroGroup(-1)
-        image = conn.getObject('Image', args.imageid)
-        size_x = image.getSizeX()
-        size_y = image.getSizeY()
-        print(image.name)
-
-        # NB: we repeat this query below for each 'page' of ROIs
-        result = roi_service.findByImage(args.imageid, opts, conn.SERVICE_OPTS)
-
-        while len(result.rois) > 0:
-            print("offset", offset)
-            print("Found ROIs:", len(result.rois))
-            for roi in result.rois:
-
-                new_roi = omero.model.RoiI()
-                new_roi.setImage(omero.model.ImageI(to_image_id, False))
-                shapes_added = False
-
-                for shape in roi.copyShapes():
-
-                    if not isinstance(shape, omero.model.MaskI):
-                        continue
-                    # assume shape is a Mask
-                    np_mask, dims = mask_to_binim_yx(shape)
-                    print('shape', np_mask.shape)
-                    t, c, z, y, x, h, w = dims
-                    print('dims', dims)
-                    image = np.zeros((size_y, size_x))
-                    image[y:y+h, x:x+w] = np_mask
-                    contours = measure.find_contours(image, 0.5)
-                    print('Found contours:', len(contours))
-                    if len(contours) > 0:
-                        contour = get_longest_contour(contours)
-                        # Only add 1 Polygon per Mask Shape.
-                        # First is usually the longest
-                        add_polygon(new_roi, contour, 0, 0, z, t)
-                    shapes_added = True
-
-                if shapes_added:
-                    update_service.saveObject(new_roi)
-
-            offset += PAGE_SIZE
-            opts.offset = rint(offset)
-            result = roi_service.findByImage(args.imageid, opts,
-                                             conn.SERVICE_OPTS)
+        source_images = []
+        target_image_ids = []
+
+        source = args.source
+        source_id = int(source.split(":")[1])
+        target = args.target
+        target_id = int(target.split(":")[1])
+
+        if source.startswith('Image:'):
+            source_images.append(conn.getObject('Image', source_id))
+            target_image_ids.append(target_id)
+        elif source.startswith('Dataset:'):
+            dataset = conn.getObject('Dataset', source_id)
+            target_dataset = conn2.getObject('Dataset', target_id)
+            ids_by_name = image_ids_by_name(target_dataset)
+            for image in dataset.listChildren():
+                if image.name in ids_by_name:
+                    source_images.append(image)
+                    target_image_ids.append(ids_by_name[image.name])
+        else:
+            print("Source needs to be Image:ID or Dataset:ID")
+
+        print("Processing", source_images)
+        print("...to target images:", target_image_ids)
+        for image, to_target_id in zip(source_images, target_image_ids):
+            process_image(conn, conn2, image, to_target_id)
 
         conn2.close()
 
 
 if __name__ == '__main__':
     # First, login to source OMERO $ omero login
-    # Copy to target server, with Image IDs
-    # $ python copy_masks_2_polygons.py user pass server FROM_IID TO_IID
+    # Copy to target server, with source and target. e.g. Image:123 Image:456
+    # $ python copy_masks_2_polygons.py user pass server FROM_TARGET TO_TARGET
     main(sys.argv[1:])

From b79e0e5d75055c622bbb905ccb373ebfdc6ad4bc Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 22 Jun 2021 12:12:19 +0100
Subject: [PATCH 14/18] Update idr0079-data-prep.md

---
 maintenance/preparation/idr0079-data-prep.md  |  19 ++-
 .../idr0079_csv_to_table_on_project.py        | 161 ++++++++++++++++++
 2 files changed, 171 insertions(+), 9 deletions(-)
 create mode 100644 maintenance/scripts/idr0079_csv_to_table_on_project.py

diff --git a/maintenance/preparation/idr0079-data-prep.md b/maintenance/preparation/idr0079-data-prep.md
index 35a0832a..e3b82603 100644
--- a/maintenance/preparation/idr0079-data-prep.md
+++ b/maintenance/preparation/idr0079-data-prep.md
@@ -77,28 +77,29 @@ Copy Masks to Polygons
 
 The idr0079 images in IDR have Masks, but we want to use Polygons in OMERO.figure.
 Use the [copy_masks_2_polygons.py](../scripts/copy_masks_2_polygons.py) script to
-convert. NB: requires `skimage`. We want to copy to each of the 5-star rated
-images above, in turn, from the ID of the corresponding Image to the local Image ID
+convert. NB: requires `skimage`. We can process an Image or a Dataset at a time:
 
     # login to IDR
     $ omero login
-    # copy to local server
-    $ python copy_masks_2_polygons.py username password server FROM_IMAGE_ID TO_IMAGE_ID
+
+    # copy from IDR e.g Dataset:1 to local server TARGET e.g. Dataset:2
+    $ python copy_masks_2_polygons.py username password server Dataset:1 Dataset:2
 
 Create OMERO.tables
 ===================
 
 We use the tsv files in https://github.com/IDR/idr0079-hartmann-lateralline to create
 an OMERO.table on the Project, with one row per Image, summarising the stats for all the
-ROIs in that Image. This uses [csv_to_table_on_project.py](https://github.com/will-moore/idr0079-hartmann-lateralline/blob/csv_to_tables_scripts/scripts/csv_to_table_on_project.py)
+ROIs in that Image. This uses [idr0079_csv_to_table_on_project.py](../scripts/idr0079_csv_to_table_on_project.py)
 
-Clone the github repo, then:
+Clone the `idr0079-hartmann-lateralline` github repo, then:
 
     $ cd idr0079-hartmann-lateralline
-    $ python scripts/csv_to_table_on_project.py
+    $ python /path/to/training-scripts/maintenance/scripts/csv_to_table_on_project.py
 
 We then create an OMERO.table on each Image that has ROIs added above:
 Use the optional `--name NAME` to run on a single named Image:
 
-    $ python scripts/csv_to_roi_table
-
+    $ cd idr0079-hartmann-lateralline
+    # process ALL raw images (use --name NAME to process 1 image)
+    $ python scripts/csv_to_roi_table.py
diff --git a/maintenance/scripts/idr0079_csv_to_table_on_project.py b/maintenance/scripts/idr0079_csv_to_table_on_project.py
new file mode 100644
index 00000000..7c425ccd
--- /dev/null
+++ b/maintenance/scripts/idr0079_csv_to_table_on_project.py
@@ -0,0 +1,161 @@
+#!/usr/bin/env python
+
+import pandas
+import csv
+import mimetypes
+import os
+
+import omero.clients
+import omero.cli
+import omero
+from omero_metadata.populate import ParsingContext
+from omero.util.metadata_utils import NSBULKANNOTATIONSRAW
+
+
+project_name = "idr0079-hartmann-lateralline/experimentA"
+
+# NB: Need to checkout https://github.com/IDR/idr0079-hartmann-lateralline
+# and run this from in idr0079-hartmann-lateralline directory OR update
+# tables_path to point to that repo.
+
+tables_path = "./experimentA/idr0079_experimentA_extracted_measurements/%s/"
+# Lots of tsv files to choose from...
+# e.g. Tissue Frame Of Reference Primary Component Analysis measured:
+# tables_path += "%s_shape_TFOR_pca_measured.tsv"
+# e.g. Other Measurements:
+tables_path += "%s_other_measurements.tsv"
+
+
+def get_omero_col_type(col_name):
+    """Returns s for string, d for double, l for long/int"""
+    if "Name" in col_name:
+        return "s"
+    return "d"
+
+
+def populate_metadata(project, dict_data):
+
+    csv_columns = list(dict_data[0].keys())
+    # Dataset Name, Image Name, PC...
+    csv_columns.sort()
+    # header s,s,d,d,d,...
+    col_types = [get_omero_col_type(name) for name in csv_columns]
+    header = f"# header {','.join(col_types)}\n"
+    print('header', header)
+    csv_file = "other_measurements_summaries.csv"
+    print("writing to", csv_file)
+    with open(csv_file, 'w') as csvfile:
+        # header s,s,d,l,s
+        csvfile.write(header)
+        writer = csv.DictWriter(csvfile, fieldnames=csv_columns)
+        writer.writeheader()
+        for data in dict_data:
+            writer.writerow(data)
+
+    # Links the csv file to the project and parses it to create OMERO.table
+    mt = mimetypes.guess_type(csv_file, strict=False)[0]
+    fileann = conn.createFileAnnfromLocalFile(
+        csv_file, mimetype=mt, ns=NSBULKANNOTATIONSRAW
+    )
+    fileid = fileann.getFile().getId()
+    project.linkAnnotation(fileann)
+    client = project._conn.c
+    ctx = ParsingContext(
+        client, project._obj, fileid=fileid, file=csv_file, allow_nan=True
+    )
+    ctx.parse()
+
+
+def process_image(image):
+
+    # Read csv for each image
+    image_name = image.name
+    table_pth = tables_path % (image_name, image_name)
+    print('table_pth', table_pth)
+    df = pandas.read_csv(table_pth, delimiter="\t")
+
+    cols = ["Source Name",
+        "Cell ID",
+        "Centroids RAW X",
+        "Centroids RAW Y",
+        "Centroids RAW Z",
+        "Centroids TFOR X",
+        "Centroids TFOR Y",
+        "Centroids TFOR Z",
+        "Longest Extension",
+        "Major Axis Length",
+        "Major/Medium Axis Eccentricity",
+        "Major/Minor Axis Eccentricity",
+        "Medium Axis Length",
+        "Medium/Minor Axis Eccentricity",
+        "Minor Axis Length",
+        "Orientation along X",
+        "Orientation along Y",
+        "Orientation along Z",
+        "Roundness (Smoothness)",
+        "Sphericity",
+        "Surface Area",
+        "Volume",
+        "X Axis Length",
+        "Y Axis Length",
+        "Y/X Aspect Ratio",
+        "Z Axis Length",
+        "Z/X Aspect Ratio",
+        "Z/Y Aspect Ratio"]
+
+    summary = df.describe()
+    data = {'count': summary['Cell ID']['count']}
+    # get: RAW_Y_Range, RAW_X_Range, RAW_Z_Range
+    for dim in ['X', 'Y', 'Z']:
+        min_val = summary[f'Centroids RAW {dim}']['min']
+        max_val = summary[f'Centroids RAW {dim}']['max']
+        data[f'RAW_{dim}_Range'] = max_val - min_val
+        min_tfor = summary[f'Centroids TFOR {dim}']['min']
+        max_tfor = summary[f'Centroids TFOR {dim}']['max']
+        data[f'TFOR_{dim}_Range'] = max_tfor - min_tfor
+    
+    # Mean_Sphericity, Mean_Volume, Mean_Z_Axis_Length, Mean_X_Axis_Length
+    for col_name in ['Sphericity', 'Volume', 'X Axis Length', 'Y Axis Length', 'Z Axis Length']:
+        value = summary[col_name]['mean']
+        data[f'Mean_{col_name}'.replace(' ', '_')] = value
+
+    # For PC .tsf
+    # columns are named "PC 1", "PC 2" etc...
+    # for pc_id in range(1,4):
+    #     for stat in ['count', 'mean', 'min', 'max', 'std']:
+    #         # No spaces in OMERO.table col names!
+    #         omero_table_colname = f"PC{pc_id}_{stat}"
+    #         value = summary[f'PC {pc_id}'][stat]
+    #         data[omero_table_colname] = value
+
+    return data
+
+
+def main(conn):
+
+    project = conn.getObject("Project", attributes={"name": project_name})
+    print("Project", project.id)
+    conn.SERVICE_OPTS.setOmeroGroup(project.getDetails().group.id.val)
+    data_rows = []
+    # For each Image in Project, open the local CSV and summarise to one row
+    for dataset in project.listChildren():
+        for image in dataset.listChildren():
+            # ignore _seg images etc.
+            if '_' in image.name:
+                continue
+            dict_data = process_image(image)
+            dict_data['Dataset Name'] = dataset.name
+            dict_data['Image Name'] = image.name
+            data_rows.append(dict_data)
+
+    populate_metadata(project, data_rows)
+
+# Usage:
+# cd idr0079-hartmann-lateralline
+# python scripts/csv_to_table_on_project.py
+
+if __name__ == "__main__":
+    with omero.cli.cli_login() as c:
+        conn = omero.gateway.BlitzGateway(client_obj=c.get_client())
+        main(conn)
+        conn.close()

From be45d3bc03e1970b450e1a5acba022c50361836e Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 1 Sep 2021 14:52:12 +0100
Subject: [PATCH 15/18] Revert --ignore_datasets changes to
 idr_get_map_annotations.py

These changes weren't needed when all of idr0079 was imported on Training server
---
 .../scripts/idr_get_map_annotations.py        | 60 ++++++-------------
 1 file changed, 19 insertions(+), 41 deletions(-)

diff --git a/maintenance/scripts/idr_get_map_annotations.py b/maintenance/scripts/idr_get_map_annotations.py
index a6ead8d4..0d20b8ae 100644
--- a/maintenance/scripts/idr_get_map_annotations.py
+++ b/maintenance/scripts/idr_get_map_annotations.py
@@ -48,21 +48,13 @@ def get_idr_datasets_as_dict(project_id):
     return by_name
 
 
-def get_idr_images_as_dict(obj_id, dtype="Dataset"):
+def get_idr_images_as_dict(dataset_id):
     """Get a dict of {name: {id: 1}} for Images in IDR Dataset."""
+    url = webclient_api_url + "images/?id=%s" % dataset_id
+    images = session.get(url).json()['images']
     by_name = {}
-    if dtype == "Dataset":
-        dataset_ids = [obj_id]
-    elif dtype == "Project":
-        datasets_url = webclient_api_url + "datasets/?id=%s" % obj_id
-        datasets = session.get(datasets_url).json()['datasets']
-        dataset_ids = [d['id'] for d in datasets]
-        print('dataset_ids', dataset_ids)
-    for dataset_id in dataset_ids:
-        url = webclient_api_url + "images/?id=%s" % dataset_id
-        images = session.get(url).json()['images']
-        for i in images:
-            by_name[i['name']] = i
+    for i in images:
+        by_name[i['name']] = i
     return by_name
 
 
@@ -81,22 +73,19 @@ def get_idr_wells_as_grid(plate_id):
     return session.get(url).json()['grid']
 
 
-def annotate_project(conn, local_id, idr_id, ignore_datasets=False):
+def annotate_project(conn, local_id, idr_id):
     project = conn.getObject("Project", local_id)
-    idr_images = {}
-    if ignore_datasets:
-        idr_images = get_idr_images_as_dict(idr_id, "Project")
-    else:
-        idr_datasets = get_idr_datasets_as_dict(idr_id)
+    idr_datasets = get_idr_datasets_as_dict(idr_id)
     for dataset in project.listChildren():
+
         print("\n\nDataset", dataset.id, dataset.name)
-        if not ignore_datasets:
-            # Get IDR Dataset with same name:
-            idr_dataset = idr_datasets.get(dataset.name)
-            if idr_dataset is None:
-                print("    NO IDR Dataset found!")
-                continue
-            idr_images = get_idr_images_as_dict(idr_dataset['id'])
+        # Get IDR Dataset with same name:
+        idr_dataset = idr_datasets.get(dataset.name)
+        if idr_dataset is None:
+            print("    NO IDR Dataset found!")
+            continue
+
+        idr_images = get_idr_images_as_dict(idr_dataset['id'])
         for image in dataset.listChildren():
 
             print("Image", image.id, image.name)
@@ -149,16 +138,7 @@ def annotate_plate(conn, plate, idr_plate_id):
         add_new_map_anns(conn, well, url)
 
 
-def run(args):
-
-    username = args.username
-    password = args.password
-    idr_obj = args.idr_obj
-    local_obj = args.local_obj
-    host = args.server
-    port = args.port
-    ignore_datasets = args.ignore_datasets
-    print('ignore_datasets', ignore_datasets)
+def run(username, password, idr_obj, local_obj, host, port):
 
     conn = BlitzGateway(username, password, host=host, port=port)
     try:
@@ -175,7 +155,7 @@ def run(args):
             return
         local_id = local_obj.split(':')[1]
         if dtype == 'Project':
-            annotate_project(conn, local_id, idr_id, ignore_datasets)
+            annotate_project(conn, local_id, idr_id)
         elif dtype == 'Plate':
             plate = conn.getObject('Plate', local_id)
             annotate_plate(conn, plate, idr_id)
@@ -203,14 +183,12 @@ def main(args):
     parser.add_argument('password')
     parser.add_argument('idr_obj', help=obj_help),
     parser.add_argument('local_obj', help=obj_help)
-    parser.add_argument(
-        '--ignore_datasets', action='store_true',
-        help="Can ignore Dataset names IF Images have unique names in Project")
     parser.add_argument('--server', default="workshop.openmicroscopy.org",
                         help="OMERO server hostname")
     parser.add_argument('--port', default=4064, help="OMERO server port")
     args = parser.parse_args(args)
-    run(args)
+    run(args.username, args.password, args.idr_obj, args.local_obj,
+        args.server, args.port)
 
 
 if __name__ == '__main__':

From 20cc22e40b33e03bb7e991021379253f04b3ed21 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 1 Sep 2021 15:06:39 +0100
Subject: [PATCH 16/18] Update idr0079-data-prep.md wrt merged PRs

---
 maintenance/preparation/idr0079-data-prep.md | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/maintenance/preparation/idr0079-data-prep.md b/maintenance/preparation/idr0079-data-prep.md
index e3b82603..649ae3ad 100644
--- a/maintenance/preparation/idr0079-data-prep.md
+++ b/maintenance/preparation/idr0079-data-prep.md
@@ -69,8 +69,9 @@ Set Pixel Sizes
 ==========================================
 
 See the commands used for IDR at [idr0079_voxel_sizes.sh]
-(https://github.com/will-moore/idr0079-hartmann-lateralline/blob/voxel_sizes/scripts/idr0079_voxel_sizes.sh)
-and run these commands on the local server, using the appropriate Dataset IDs.
+(https://github.com/IDR/idr0079-hartmann-lateralline/blob/master/scripts/idr0079_voxel_sizes.sh)
+and run these commands on the local server, using the appropriate Dataset IDs, at least
+for the Datasets you wish to use.
 
 Copy Masks to Polygons
 ======================
@@ -89,7 +90,7 @@ Create OMERO.tables
 ===================
 
 We use the tsv files in https://github.com/IDR/idr0079-hartmann-lateralline to create
-an OMERO.table on the Project, with one row per Image, summarising the stats for all the
+an OMERO.table on the Project (for use with OMERO.parade), with one row per Image, summarising the stats for all the
 ROIs in that Image. This uses [idr0079_csv_to_table_on_project.py](../scripts/idr0079_csv_to_table_on_project.py)
 
 Clone the `idr0079-hartmann-lateralline` github repo, then:
@@ -97,9 +98,10 @@ Clone the `idr0079-hartmann-lateralline` github repo, then:
     $ cd idr0079-hartmann-lateralline
     $ python /path/to/training-scripts/maintenance/scripts/csv_to_table_on_project.py
 
-We then create an OMERO.table on each Image that has ROIs added above:
+We then create an OMERO.table on each Image that has ROIs added above, using
+the `_other_measurements.tsv` table for each Image.
 Use the optional `--name NAME` to run on a single named Image:
 
     $ cd idr0079-hartmann-lateralline
     # process ALL raw images (use --name NAME to process 1 image)
-    $ python scripts/csv_to_roi_table.py
+    $ python scripts/csv_to_roi_table.py _other_measurements.tsv

From df286ab55b772a95906e169a2de2299c500a7b9f Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 1 Sep 2021 15:07:55 +0100
Subject: [PATCH 17/18] Revert unused changes to calibrate_images.py

---
 maintenance/scripts/calibrate_images.py | 117 ++++++------------------
 1 file changed, 27 insertions(+), 90 deletions(-)

diff --git a/maintenance/scripts/calibrate_images.py b/maintenance/scripts/calibrate_images.py
index 453d2a34..5654a6c2 100644
--- a/maintenance/scripts/calibrate_images.py
+++ b/maintenance/scripts/calibrate_images.py
@@ -33,50 +33,9 @@
 from omero.model.enums import UnitsLength
 
 
-def setPixelSize(conn, image, value, unit):
-    print('Image', image.id, value)
-    value_z = None
-    if 'x' in value:
-        value_xy = float(value.split('x')[0])
-        value_z = float(value.split('x')[1])
-    else:
-        value_xy = float(value)
-    xy = omero.model.LengthI(value_xy, getattr(UnitsLength, unit))
-    p = image.getPrimaryPixels()._obj
-    p.setPhysicalSizeX(xy)
-    p.setPhysicalSizeY(xy)
-    if value_z is not None:
-        z = omero.model.LengthI(value_z, getattr(UnitsLength, unit))
-        p.setPhysicalSizeZ(z)
-    conn.getUpdateService().saveObject(p)
-
-
-def set_by_target_id(password, username, target, host, port, value, unit):
-
-    conn = BlitzGateway(username, password, host=host, port=port)
-    conn.connect()
-    target_type = target.split(':')[0]
-    target_id = int(target.split(':')[1])
-    if target_type not in ['Project', 'Dataset', 'Image']:
-        print("Target must be Project:ID, Dataset:ID or Image:ID")
-        return
-    images = []
-    if target_type == "Project":
-        for dataset in conn.getObject('Project', target_id).listChildren():
-            images.extend((list(dataset.listChildren())))
-    elif target_type == "Dataset":
-        images = list(conn.getObject('Dataset', target_id).listChildren())
-    elif target_type == "Image":
-        images = [conn.getObject("Image", target_id)]
-    print('images', images)
-
-    for image in images:
-        setPixelSize(conn, image, value, unit)
-
-
-def set_for_users_by_dataset_name(password, target, host, port, value, unit):
-
-    for i in range(1, 2):
+def run(password, target, host, port):
+
+    for i in range(1, 51):
 
         username = "user-%s" % i
         print(username)
@@ -95,66 +54,44 @@ def set_for_users_by_dataset_name(password, target, host, port, value, unit):
                 print("No dataset with name %s found" % target)
                 continue
 
+            dataset_obj = dataset[0]
             datasetId = dataset[0].getId().getValue()
+
             print('dataset', datasetId)
-            for image in conn.getObject("Dataset", datasetId).listChildren():
-                setPixelSize(conn, image, value, unit)
+            params2 = omero.sys.ParametersI()
+            params2.addId(dataset_obj.getId())
+            query = "select l.child.id from DatasetImageLink \
+                     l where l.parent.id = :id"
+            images = service.projection(query, params2, conn.SERVICE_OPTS)
+            values = []
+            for k in range(0, len(images)):
+
+                image_id = images[k][0].getValue()
+                image = conn.getObject("Image", image_id)
+
+                u = omero.model.LengthI(0.33, UnitsLength.MICROMETER)
+                p = image.getPrimaryPixels()._obj
+                p.setPhysicalSizeX(u)
+                p.setPhysicalSizeY(u)
+                values.append(p)
+
+            if len(images) > 0:
+                conn.getUpdateService().saveArray(values)
         except Exception as exc:
             print("Error during calibration: %s" % str(exc))
         finally:
             conn.close()
 
 
-def run(args):
-    password = args.password
-    target = args.target
-    value = args.value
-    unit = args.unit
-    host = args.server
-    port = args.port
-
-    # Handle target is e.g. "Project:1"
-    if ':' in target:
-        try:
-            int(target.split(':')[1])
-            set_by_target_id(password, args.user, target, host, port,
-                             value, unit)
-            return
-        except ValueError:
-            print("Not valid Project or Dataset ID")
-
-    # Assume that target was a Dataset Name
-    set_for_users_by_dataset_name(password, target, host, port, value, unit)
-
-
 def main(args):
-    """
-    The script sets Pixels Sizes in 2 use-cases.
-    Each needs a pixel size 'value' eg. 0.85 for X and Y or
-    '0.85x0.2' for XY and Z.
-    Units are optional. Default is "MICROMETER".
-
-    1) For many users 'user-1...user-50' etc with a NAMED Dataset
-    $ calibrate_images.py [password] [dataset_name] [value] --server [host]
-
-    2) For a single user, where the target is Project:ID or Dataset:ID
-    calibrate_images.py [pass] [target] [value] --user [name] --server [host]
-    """
     parser = argparse.ArgumentParser()
     parser.add_argument('password')
-    parser.add_argument(
-        'target',
-        help="Dataset name (for many users) or Project/Dataset/Image:ID")
-    parser.add_argument('value', help="Pixel size value")
-    parser.add_argument('--unit', default="MICROMETER",
-                        help="Unit from omero.")
-    parser.add_argument('--user', help="Username ONLY if single user")
-    parser.add_argument('--server', default="localhost",
+    parser.add_argument('target')
+    parser.add_argument('--server', default="workshop.openmicroscopy.org",
                         help="OMERO server hostname")
     parser.add_argument('--port', default=4064, help="OMERO server port")
     args = parser.parse_args(args)
-
-    run(args)
+    run(args.password, args.target, args.server, args.port)
 
 
 if __name__ == '__main__':

From 083298950632037e33d725948ec59e5efb522cc2 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 1 Sep 2021 16:07:07 +0100
Subject: [PATCH 18/18] Remove figure_image_table_shape_heatmap.js

This is now in omero-guide-figure
---
 .../figure_image_table_shape_heatmap.js       | 60 -------------------
 1 file changed, 60 deletions(-)
 delete mode 100644 practical/javascript/figure_image_table_shape_heatmap.js

diff --git a/practical/javascript/figure_image_table_shape_heatmap.js b/practical/javascript/figure_image_table_shape_heatmap.js
deleted file mode 100644
index 2ef94f69..00000000
--- a/practical/javascript/figure_image_table_shape_heatmap.js
+++ /dev/null
@@ -1,60 +0,0 @@
-
-//
-// Copyright (C) 2021 University of Dundee & Open Microscopy Environment.
-// All rights reserved.
-//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU Affero General Public License as
-// published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
-//
-// You should have received a copy of the GNU Affero General Public License
-// along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-// Using the browser devtools to manipulate OMERO.figure is an experimental
-// feature for developers.
-// N.B.: Never paste untrusted code into your browser console.
-//
-// This script requires an OMERO.table linked to the Image
-// with a 'Shape' column and another numerical named column (edit below).
-// Select panel with Shapes added from OMERO (shape.id should be in the table).
-// This colors each Shape according to a heatmap for the named column.
-
-async function shapeData(panel) {
-    const shapeIds = panel.get("shapes").map(s => s.id).filter(id => id > 0);
-    console.log('shapeIds', shapeIds);
-    let vals_by_shape = {};
-    for (let i = 0; i < shapeIds.length; i++) {
-        // Load one at a time - more reliable
-        let url = `/webgateway/table/Image/${panel.get('imageId')}/query/?query=Shape-${shapeIds[i]}`;
-        let r = await fetch(url).then(rsp => rsp.json());
-        let colIndex = r.data?.columns?.indexOf("Centroids_RAW_X");
-        let shapeIndex = r.data?.columns?.indexOf("Shape");
-        if (colIndex && shapeIndex && r.data?.rows.length > 0) {
-            console.log("Value", r.data.rows[0][colIndex]);
-            vals_by_shape[r.data.rows[0][shapeIndex]] = r.data.rows[0][colIndex];
-        }
-    };
-    // Once all loaded, we can calculate range and assign colours to shapes
-    const values = Object.values(vals_by_shape);
-    let minVal = Math.min(...values);
-    let valRange = Math.max(...values) - minVal;
-    console.log('min, range', minVal, valRange);
-    const new_shapes = panel.get("shapes").map(shape => {
-        // hide any shapes we don't have data for
-        if (!vals_by_shape[shape.id]) return { ...shape, strokeWidth: 0.01 };
-        let value = (vals_by_shape[shape.id] - minVal) / valRange;
-        let red = parseInt(value * 255).toString(16);
-        let blue = (255 - parseInt(value * 255)).toString(16);
-        red = red.length == 1 ? `0` + red : red;
-        blue = blue.length == 1 ? `0` + blue : blue;
-        return { ...shape, strokeColor: `#${red}00${blue}`, strokeWidth: 5 }
-    });
-    panel.set('shapes', new_shapes);
-}
-figureModel.getSelected().forEach(shapeData);