Merge pull request #8 from NFDI4BIOIMAGE/dev

Support for multiple images

.omeroci/app-config

@@ -0,0 +1,11 @@
+#! /usr/bin/env bash
+source /infra/utils
+set -e
+set +u
+cd $TARGET
+# add the app to omero.web.apps
+value=$(get_app_name)
+# Configuration commands
+
+su - omero-web -c "env OMERODIR=$OMERODIR /opt/omero/web/venv3/bin/omero config set omero.web.apps '[\"$value\"]'"
+su - omero-web -c "env OMERODIR=$OMERODIR /opt/omero/web/venv3/bin/omero config set omero.web.omero_vitessce.serveraddress '"http://localhost:4080"'"

README.md

@@ -91,7 +91,7 @@ Only files attached to the dataset/image are available in the form.
 
 The following fields are available:
 - `Config file name`    (required, "VitessceConfig-YYYY.MM.DD_HHMMSS.json"): Name of the config file to attach, a ".json" extension is added if missing. 	
-- `Image`               (required): 	                                       OMERO Image to view.
+- `Images`               (required): 	                                       OMERO Image(s) to view, assumes the same pixel size for all images.
 - `Segmentation`        (optional, `None`): 	                               Label image to overlay on the image, pixel values correspond to cell identities.
 - `Cell identities`     (optional, `None`): 	                               `.csv` file with at least 2 columns: `Cell id column` and `Label column` defined in the 2 fields below. 
 - `Cell id column`      (optional, "cell_id"):   	                           Name of the `Cell id column` used in `Cell identities`, `Expression`, `Embeddings`.

omero_vitessce/forms.py

@@ -22,9 +22,9 @@ class ConfigForm(forms.Form):
 
     config_file_name_help = "Name of the config file to use, \
             a '.json' extension is added if missing."
-    image_help = "OMERO Image to view."
+    images_help = "OMERO Image(s) to view, assumes identical pixel size."
     segmentation_help = "Label image to overlay on the image, \
-            pixel values correspond to cell identities."
+            pixel values should correspond to cell identities."
     cell_identities_help = ".csv file with at least 2 columns: \
             Cell id column and Label column defined in the 2 fields below."
     cell_id_help = "Name of the Cell id column used in \
@@ -60,19 +60,21 @@ def __init__(self, file_names, file_urls,
         self.text_choices, self.image_choices = self.prepare_choices(
                 file_names, file_urls, img_names, img_urls)
 
+        # Configuration file fields
         filename = self.make_config_file_name()
 
         self.fields["config_file_name"] = forms.CharField(
                 empty_value=filename, strip=True,
                 min_length=1, max_length=40, required=False,
                 help_text=ConfigForm.config_file_name_help)
 
+        # images field
         # No empty default, we alway want an image in the config
-        self.fields["image"] = forms.ChoiceField(
+        self.fields["images"] = forms.MultipleChoiceField(
                 choices=self.image_choices[1:], required=True,
-                help_text=ConfigForm.image_help)
+                help_text=ConfigForm.images_help)
 
-        # Cell data
+        # Cell data fields
         self.fields["segmentation"] = forms.ChoiceField(
                 choices=self.image_choices, required=False,
                 help_text=ConfigForm.segmentation_help)
@@ -109,7 +111,7 @@ def __init__(self, file_names, file_urls,
                 min_length=1, max_length=20, required=False,
                 help_text=ConfigForm.embeddings_y_help)
 
-        # Molecule data
+        # Molecule data fields
         self.fields["molecules"] = forms.ChoiceField(
                 choices=self.text_choices, required=False,
                 help_text=ConfigForm.molecules_help)

omero_vitessce/omero_vitessce_settings.py

@@ -13,7 +13,7 @@ def str_not_empty(o):
 
 OMEROVITESSCE_SETTINGS_MAPPINGS = {
     'omero.web.omero_vitessce.serveraddress': ['SERVER_ADDRESS',
-                                               '"http://localhost:4080"',
+                                               '""',
                                                str_not_empty, None]
 }
 

omero_vitessce/templates/omero_vitessce/vitessce_panel.html

@@ -62,10 +62,10 @@
 							Images</th>
 					</tr>
 					<tr>
-						<th><div class="tooltip">{{ form.image.label_tag }}
-							<span class="tooltiptext">{{ form.image.help_text }}</span>
+						<th><div class="tooltip">{{ form.images.label_tag }}
+							<span class="tooltiptext">{{ form.images.help_text }}</span>
 						</div></th>
-						<th style="text-align:left;">{{ form.image }}</th>
+						<th style="text-align:left;">{{ form.images }}</th>
 					<tr style="height:30px">
 						<th colspan="2" style="text-align:center;vertical-align:bottom">
 							Cell Data</th>

omero_vitessce/utils.py

@@ -3,6 +3,7 @@
 
 from omero.util.temp_files import create_path
 
+from .forms import ConfigForm
 from . import omero_vitessce_settings
 
 from vitessce import VitessceConfig, OmeZarrWrapper, MultiImageWrapper
@@ -149,14 +150,26 @@ def create_config(config_args, obj_type, obj_id, conn):
     the results from the form are used as args.
     """
 
+    # If an attachment/image is deleted/moved between the Vitessce right tab
+    # plugin is loaded and the form is submitted then it will not be found
+    # and will not be present in the cleaned_data -> None
+    file_names, file_urls, img_files, img_urls = get_files_images(
+        obj_type, obj_id, conn)
+    config_args = ConfigForm(data=config_args, file_names=file_names,
+                             file_urls=file_urls, img_names=img_files,
+                             img_urls=img_urls)
+    config_args = config_args.cleaned_data
+
     description, name = get_details(obj_type, obj_id, conn)
 
     vc = VitessceConfig(schema_version="1.0.16",
                         name=name, description=description)
     vc_dataset = vc.add_dataset()
 
-    img_url = config_args.get("image")
-    images = [OmeZarrWrapper(img_url=img_url, name="Image")]
+    images = []
+    img_urls = config_args.get("images")
+    for n, img_url in enumerate(img_urls):
+        images.append(OmeZarrWrapper(img_url=img_url, name=f"Image {n}"))
 
     sp = vc.add_view(Vt.SPATIAL, dataset=vc_dataset)
     lc = vc.add_view(Vt.LAYER_CONTROLLER, dataset=vc_dataset)

omero_vitessce/views.py

@@ -38,7 +38,8 @@ def vitessce_panel(request, obj_type, obj_id, conn=None, **kwargs):
     if OMERO_WEB_ZARR:
         files, urls, img_files, img_urls = get_files_images(
                 obj_type, obj_id, conn)
-        form = ConfigForm(files, urls, img_files, img_urls)
+        form = ConfigForm(file_names=files, file_urls=urls,
+                          img_names=img_files, img_urls=img_urls)
         context["form"] = form
     else:
         context["form"] = None