Fix parade prep notes

maintenance/preparation/idr0021-data-prep.md

@@ -43,57 +43,47 @@ In the webclient, create a Project 'idr0021' and add the 10 new Datasets created
 Add Map Annotations from IDR
 ============================
 
-Edit the script [idr_get_map_annotations.py](../scripts/idr_get_map_annotations.py) with the ID of the 'idr0021' Project created
-above. This will get map annotations from all images in the [idr0021](https://idr.openmicroscopy.org/webclient/?show=project-51) and create identical map annotations on the corresponding images.
+Run the script [idr_get_map_annotations.py](../scripts/idr_get_map_annotations.py) with the ID of the 'idr0021' Project created
+above. See the script for usage details. This will get map annotations from all images in the [idr0021](https://idr.openmicroscopy.org/webclient/?show=project-51) 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.
-Edit the ```project_id``` and run the [channel_names_from_maps.py](../scripts/channel_names_from_maps.py)
-script on the local data.
+Run the [channel_names_from_maps.py](../scripts/channel_names_from_maps.py)
+script on the local data, passing in the `Project ID`.
 
 
 Analyse in Fiji and save ROIs in OMERO
 ======================================
 
-Run [analyse_particles_for_another_user.jy](../../practical/jython/analyse_particles_for_another_user.jy) in Fiji with the
-appropriate credentials on a Dataset at a time, updating the dataset_id each time.
+First we need to delete an Image that is the only Z-stack and is analyzed differently from the others:
+```NEDD1ab_NEDD1141_I_012_SIR.dv``` in Dataset ```NEDD1-C1```.
 
-This will Analyse Particles and create ROIs on all channels of each Image.
+Run [idr0021.groovy](https://github.com/ome/omero-guide-fiji/blob/master/scripts/groovy/idr0021.groovy) in Fiji with the
+appropriate credentials on the `idr0021` Project.
 
-This script also creates a summary OMERO.table one row per image containing measurements results
-e.g. the bounding box of the biggest ROI.
-The table is linked to the Project. The output is also saved as a CSV file and linked to the Project.
+This will Analyse Particles and create ROIs on all channels of each Image, using Channel names to pick the correct
+Channel for each Image.
 
-
-Create Map Annotations and Table from ROIs
-==========================================
-
-First we need to delete an outlier Image that causes
-[problems in OMERO.parade](https://github.com/ome/omero-parade/issues/26). Delete
-```NEDD1ab_NEDD1141_I_012_SIR```. This image is the only Z-stack and no blobs are found
-so the Polygon created covers the whole plane.
-
-The [batch_roi_export_to_table.py](../../practical/python/server/batch_roi_export_to_table.py) script needs to be installed on the server. Run this from the webclient, selecting the ```idr0021``` Project to create a single Table on this Project, that has rows for all Images in the Project.
-
-This script uses the Channel Names to pick a Channel that matches the Dataset name
-for each Image. This is the Channel that needs to be analysed and is used to filter Shapes created
-by Fiji.
-
-This script also creates Map annotations and can create a CSV (could be shown in workshop).
-Options for these are handled by checkboxes at the bottom of the script dialog.
+This script also creates a summary OMERO.table on the `idr0021` Project, named `Summary_from_Fiji`.
+This can be seen under the `Attachments` tab for the Project, with an `eye` icon that will open the table.
+The table has one row per image containing measurements results
+e.g. the area of the bounding box of the biggest ROI.
+The output is also saved as a CSV file and linked to the Project.
 
 
 Delete ROIs and Map annotations for 1 Dataset
 =============================================
 
-Edit and run the following scripts on the first Dataset
-to remove Map Annotations and ROIs from all Images in that Dataset so we can show them being
-created in the workshop:
+If you wish to remove ROIs from all Images in a Dataset so we can show them being
+created in the workshop use the Dataset ID:
+
+	$ omero delete Dataset/Image/Roi:DATASET_ID
+
+If you wish to do this for all users, using the Dataset name for each user, use:
 
- - [delete_annotations.py](../scripts/delete_annotations.py)
  - [delete_ROIs.py](../scripts/delete_ROIs.py)
 
 The data is now ready to be presented in a workshop and analysed with ```OMERO.parade```.
@@ -109,9 +99,17 @@ and import this:
 
 	$ path/to/omero import INMAC384-DAPI-CM-eGFP_59223_1
 
+Alternatively, you can copy a Plate from IDR, copying only the first Z and T index of each Image, using
+[idr_copy_plate.py](../scripts/idr_copy_plate.py). This will ask for login details of the server where you 
+wish to copy the Plate. IDR [Plate 422](http://idr.openmicroscopy.org/webclient/?show=plate-422) is a
+suitable Plate:
+
+	$ python maintenance/scripts/idr_copy_plate.py 422
+
 We need to populate an OMERO.table on the Plate to demonstrate filtering with
-OMERO.parade. For that we will use the [channel_minmax_to_table.py](../scripts/channel_minmax_to_table.py). Run the command line script with the Plate ID:
+OMERO.parade. For that we will use the [channel_minmax_to_table.py](../scripts/channel_minmax_to_table.py).
+Run the command line script with the Plate ID:
 
-	$ python maintenance/scripts/channel_minmax_to_table.py username password --server server.address plate_id
+	$ python maintenance/scripts/channel_minmax_to_table.py PLATE_ID
 
 This should create an Annotation on the Plate called ``Channels_Min_Max_Intensity``.

maintenance/scripts/channel_minmax_to_table.py

@@ -21,6 +21,7 @@
 
 import argparse
 import omero
+from omero.cli import cli_login
 from omero.rtypes import rstring
 import omero.grid
 from omero.gateway import BlitzGateway
@@ -29,58 +30,57 @@
 NAMESPACE = "openmicroscopy.org/omero/bulk_annotations"
 
 
-def run(username, password, plate_id, host, port):
-
-    conn = BlitzGateway(username, password, host=host, port=port)
+def run(conn, plate_id):
+
+    query_service = conn.getQueryService()
+
+    # Create a name for the Original File
+    tablename = "Channels_Min_Max_Intensity"
+
+    # Go through all wells in Plate, adding row for each
+    plate = conn.getObject("Plate", plate_id)
+    wellIds = []
+    rowData = []
+    chCount = 0
+    for well in plate._listChildren():
+        well = omero.gateway.WellWrapper(conn, well)
+        image = well.getImage()
+        if image is None:
+            continue
+        wellIds.append(well.id)
+        chCount = image.getSizeC()
+        row = []
+        print("well, image", well.id, image.id)
+
+        params = omero.sys.ParametersI()
+        params.addId(image.getPixelsId())
+        query = """select pixels from Pixels as pixels
+                    left outer join fetch pixels.channels as channels
+                    join fetch channels.statsInfo where pixels.id=:id"""
+        result = query_service.findAllByQuery(query, params)
+
+        row = []
+        for pix in result:
+            for ch in pix.iterateChannels():
+                si = ch.statsInfo
+                row.extend([si.globalMin.val, si.globalMax.val])
+        rowData.append(row)
+
+    print('wellIds', wellIds)
+    print('rowData', rowData)
+
+    # Now we know how many channels, we can make the table
+    col1 = omero.grid.WellColumn('Well', '', [])
+    columns = [col1]
+    colNames = []
+    for chIdx in range(chCount):
+        for name in ['Ch%sMin' % chIdx, 'Ch%sMax' % chIdx]:
+            colNames.append(name)
+            columns.append(omero.grid.LongColumn(name, '', []))
+
+    table = conn.c.sf.sharedResources().newTable(1, tablename)
+    orig_file = None
     try:
-        conn.connect()
-        query_service = conn.getQueryService()
-
-        # Create a name for the Original File
-        tablename = "Channels_Min_Max_Intensity"
-
-        # Go through all wells in Plate, adding row for each
-        plate = conn.getObject("Plate", plate_id)
-        wellIds = []
-        rowData = []
-        chCount = 0
-        for well in plate._listChildren():
-            well = omero.gateway.WellWrapper(conn, well)
-            image = well.getImage()
-            if image is None:
-                continue
-            wellIds.append(well.id)
-            chCount = image.getSizeC()
-            row = []
-            print("well, image", well.id, image.id)
-
-            params = omero.sys.ParametersI()
-            params.addId(image.getPixelsId())
-            query = """select pixels from Pixels as pixels
-                       left outer join fetch pixels.channels as channels
-                       join fetch channels.statsInfo where pixels.id=:id"""
-            result = query_service.findAllByQuery(query, params)
-
-            row = []
-            for pix in result:
-                for ch in pix.iterateChannels():
-                    si = ch.statsInfo
-                    row.extend([si.globalMin.val, si.globalMax.val])
-            rowData.append(row)
-
-        print('wellIds', wellIds)
-        print('rowData', rowData)
-
-        # Now we know how many channels, we can make the table
-        col1 = omero.grid.WellColumn('Well', '', [])
-        columns = [col1]
-        colNames = []
-        for chIdx in range(chCount):
-            for name in ['Ch%sMin' % chIdx, 'Ch%sMax' % chIdx]:
-                colNames.append(name)
-                columns.append(omero.grid.LongColumn(name, '', []))
-
-        table = conn.c.sf.sharedResources().newTable(1, tablename)
         table.initialize(columns)
 
         # Add Data from above
@@ -94,37 +94,33 @@ def run(username, password, plate_id, host, port):
 
         print("Adding data: ", len(data))
         table.addData(data)
-        table.close()
 
         print("table closed...")
         orig_file = table.getOriginalFile()
-        fileAnn = omero.model.FileAnnotationI()
-        fileAnn.ns = rstring(NAMESPACE)
-        fileAnn.setFile(omero.model.OriginalFileI(orig_file.id.val, False))
-        fileAnn = conn.getUpdateService().saveAndReturnObject(fileAnn)
-        link = omero.model.PlateAnnotationLinkI()
-        link.setParent(omero.model.PlateI(plate_id, False))
-        link.setChild(omero.model.FileAnnotationI(fileAnn.id.val, False))
-
-        print("save link...")
-        conn.getUpdateService().saveAndReturnObject(link)
-
-    except Exception as exc:
-        print("Error while changing names: %s" % str(exc))
     finally:
-        conn.close()
+        table.close()
+
+    if orig_file is None:
+        print("Table creation failed")
+    fileAnn = omero.model.FileAnnotationI()
+    fileAnn.ns = rstring(NAMESPACE)
+    fileAnn.setFile(omero.model.OriginalFileI(orig_file.id.val, False))
+    fileAnn = conn.getUpdateService().saveAndReturnObject(fileAnn)
+    link = omero.model.PlateAnnotationLinkI()
+    link.setParent(omero.model.PlateI(plate_id, False))
+    link.setChild(omero.model.FileAnnotationI(fileAnn.id.val, False))
+
+    print("save link...")
+    conn.getUpdateService().saveAndReturnObject(link)
 
 
 def main(args):
     parser = argparse.ArgumentParser()
-    parser.add_argument('username')
-    parser.add_argument('password')
     parser.add_argument('plate_id')
-    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.plate_id, args.server, args.port)
+    with cli_login() as cli:
+        conn = BlitzGateway(client_obj=cli._client)
+        run(conn, args.plate_id)
 
 
 if __name__ == '__main__':

maintenance/scripts/idr_copy_plate.py

@@ -27,6 +27,7 @@
 
 import argparse
 import omero
+from omero.cli import cli_login
 from omero.gateway import BlitzGateway
 from omero.rtypes import rint, rstring
 from omero.model import PlateI
@@ -69,12 +70,8 @@ def add_images_to_plate(update_service, plate, images, row, column):
         update_service.saveObject(ws)
 
 
-def run(username, password, plate_id, host, port):
+def run(conn, plate_id):
     """Run the script."""
-    # Create connection to training server
-    conn = BlitzGateway(username, password, host=host, port=port)
-    conn.connect()
-
     # Create connection to IDR server
     # NB: conn.connect() not working on IDR. Do it like this
     idr_client = omero.client(host="idr.openmicroscopy.org", port=4064)
@@ -104,21 +101,19 @@ def run(username, password, plate_id, host, port):
         add_images_to_plate(update_service, plate, new_imgs,
                             idr_well.row, idr_well.column)
 
-    conn.close()
-    idr_conn.close()
+    print("Created Plate:", plate.id.val)
 
 
 def main(args):
     """Entry point. Parse args and run."""
     parser = argparse.ArgumentParser()
-    parser.add_argument('username')
-    parser.add_argument('password')
     parser.add_argument('plate_id')
-    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.plate_id, args.server, args.port)
+
+    with cli_login() as cli:
+        conn = BlitzGateway(client_obj=cli._client)
+        run(conn, args.plate_id)
 
 
 if __name__ == '__main__':