Merge pull request #4 from NFDI4BIOIMAGE/dev

Options for genrating configuration files.

README.md

@@ -53,36 +53,62 @@ The plugin can be used with:
 - `Open with` `->` `Vitessce` on the left side panel. 
 
 #### Right-hand-side panel:
-- **Prexisting config files**:  
-![Right-Config](https://github.com/user-attachments/assets/b8fea5f0-1d8f-4578-a577-8744d32dcaa5)   
-Clicking the link will open a new tab with the viewer displaying the selected configuration.
-- **Autogenerating config file**:  
-![Right-Auto](https://github.com/user-attachments/assets/8dfa22cc-dbb5-493d-b837-d609a11a1346)  
-Clicking the button will autogenerate a config file and attach it to the dataset/image, and the viewer displaying the autogenerated configuration.  
+- **Prexisting config files**:
+
+Clicking the link will open a new tab with the viewer displaying the selected configuration.  
+![Link-List-image](https://github.com/user-attachments/assets/b95c77a3-77c5-4221-83f2-c9c460a83f2e)  
+
+
+- **Autogenerating config file**:
+
+The form allows the user to automatically generate a config file with the selected parameters. After clicking the `Generate Config` button
+a config file is generated and attached to the dataset/image. The viewer displaying the autogenerated configuration will open in a new tab.    
+![Form-image](https://github.com/user-attachments/assets/5c81aba3-adfd-465c-86f0-9e03506ec3ea)  
 
 #### Open-with:
 Right click on a `dataset` or an `images` in the left-panel and select `open-with` -> `Vitessce`.  
 This will open the vitessce viewer in a new tab using the first configuration file attachement.
 ![Openwith-image](https://github.com/user-attachments/assets/f75cc27c-4cd3-4a19-ae20-7d8f0a47aa87)
 
 ### Viewer window
-After using a The Vitessce viewer is opened in a new tab:
-![image](https://github.com/user-attachments/assets/77de517e-67e4-42d6-a2b6-2a3a6a11dc7e)
+After autogenerating or selecting a config file, the Vitessce viewer is opened in a new tab:
+![Viewer GIF](https://github.com/user-attachments/assets/719a3093-2a6a-480d-afc9-522b4873310e)
+
+
 
 ### Config files
-The omero-vitessce plugin considers all files with the `.json.txt` extension attached to the image or dataset as config files for the viewer.
+The omero-vitessce plugin considers all files with the `.json` extension attached to the image or dataset as config files for the viewer.
 The config files should follow the vitessce view-config-json format: http://vitessce.io/docs/view-config-json/
 
 #### Autogenerated config files
 Config files can be autogenerated for:
-- `images`: A spatial view and a layer controller view are setup for the image.
-- `datasets`: All images in the dataset are bundled togheter and a spatial view and a layer controller are setup.
+- `images`
+- `datasets`
 
 Assumes that the images are in the OME-NGFF format v0.4 and that [omero-web-zarr](https://github.com/ome/omero-web-zarr) is
 available to serve the images.
+The attachements must be in `.csv` format and the column with the cell identifiers should be consistent across attachements.
+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, OME-NGFF images only.
+`Segmentation`        (optional, `None`): 	                               Segmentation to overlay on the image, OME-NGFF images only.
+`Cell identities`     (optional, `None`): 	                               `.csv` file with at least 2 columns: `Cell id column` and `Label column` defined in the 2 fileds below. 
+`Cell id column`      (optional, "cell_id"):   	                           Name of the `Cell id column` used in `Cell identities`, `Expression`, `Embeddings`.
+`Label column`        (optional, "label"): 	                               Name of the `Label` used in `Cell identities`.
+`Expression` 	      (optional, `None`):                                  `.csv` file with the `Cell id column` all other columns are considered as expression values and should be numerical.
+`Embeddings`          (optional, `None`):                                  `.csv` file with the `Cell id column` and the `Embedding x` and `Embedding y` columns defined in the 2 fileds below. 
+`Embedding x`         (optional, "UMAP_1"): 	                            Name of the `Embedding x` used in `Embeddings`.
+`Embedding y`         (optional, "UMAP_2"): 	                            Name of the `Embedding y` used in `Embeddings`.
+`Histograms`          (required , `True`): 	                                Add 3 plots showing: The number of transcripts per cell, the number of cells in each set, gene expression in each set.
+`Heatmap`             (required , `True`):                                  Adds an heatmap.
+
+The `Expression` and `Cell identities` files are required to show the histograms.  
+The `Embeddings` file is necessary to show the cells in a scatterplot.
 
 #### Custom config files
-Custom config files should have a `.json.txt` extension and added as attachements to a dataset or an image.
+Custom config files should have a `.json` extension and added as attachements to a dataset or an image.
 The configuration files does not need to refer to the dataset / image it is attached to and can refer to other images.
 
 For how to create a custom config file see:
@@ -101,6 +127,7 @@ Development
 ## Sources
 
 The main sources are:
+- omero-vitessce from Will Moore: https://github.com/will-moore/omero-vitessce
 - cookiecutter-omero-webapp: https://github.com/ome/cookiecutter-omero-webapp
 - `react_webapp` from omero-web-apps-examples: https://github.com/ome/omero-web-apps-examples/tree/master/react-webapp
 - Vitessce python package used for generating config files http://python-docs.vitessce.io/

omero_vitessce/forms.py

@@ -0,0 +1,90 @@
+import datetime
+
+from django import forms
+
+
+class ConfigForm(forms.Form):
+    """ Form used to collect the parameters used to
+        automatically generate a config file for Vitessce
+    """
+
+    default_cell_id_col = "cell_id"
+    default_label_col = "label"
+    default_embedding_x_col = "UMAP_1"
+    default_embedding_y_col = "UMAP_2"
+
+    def __init__(self, file_names, file_urls,
+                 img_names, img_urls, *args, **kwargs):
+        super(ConfigForm, self).__init__(*args, **kwargs)
+
+        self.text_choices, self.image_choices = self.prepare_choices(
+                file_names, file_urls, img_names, img_urls)
+
+        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)
+
+        # No empty default, we alway want an image in the config
+        self.fields["image"] = forms.ChoiceField(
+                choices=self.image_choices[1:], required=True)
+
+        self.fields["segmentation"] = forms.ChoiceField(
+                choices=self.image_choices, required=False)
+
+        self.fields["cell identities"] = forms.ChoiceField(
+                choices=self.text_choices, required=False)
+
+        self.fields["cell id column"] = forms.CharField(
+                empty_value=ConfigForm.default_cell_id_col, strip=True,
+                min_length=1, max_length=20, required=False)
+
+        self.fields["label column"] = forms.CharField(
+                empty_value=ConfigForm.default_label_col, strip=True,
+                min_length=1, max_length=20, required=False)
+
+        self.fields["expression"] = forms.ChoiceField(
+                choices=self.text_choices, required=False)
+
+        self.fields["embeddings"] = forms.ChoiceField(
+                choices=self.text_choices, required=False)
+
+        self.fields["embedding x"] = forms.CharField(
+                empty_value=ConfigForm.default_embedding_x_col, strip=True,
+                min_length=1, max_length=20, required=False)
+
+        self.fields["embedding y"] = forms.CharField(
+                empty_value=ConfigForm.default_embedding_y_col, strip=True,
+                min_length=1, max_length=20, required=False)
+
+        self.fields["histograms"] = forms.BooleanField(initial=True,
+                                                       required=False)
+        self.fields["heatmap"] = forms.BooleanField(initial=True,
+                                                    required=False)
+
+        # Set default values for CharField fields
+        self.fields["config file name"].initial = filename
+        self.fields["cell id column"].initial = ConfigForm.default_cell_id_col
+        self.fields["label column"].initial = ConfigForm.default_label_col
+        self.fields["embedding x"].initial = ConfigForm.default_embedding_x_col
+        self.fields["embedding y"].initial = ConfigForm.default_embedding_y_col
+
+    def make_config_file_name(self):
+        """ Creates the default config file name with a timestamp:
+        VitessceConfig-yyyy.mm.dd_hhmmss.json
+        """
+        ts = datetime.datetime.now().strftime("%Y.%m.%d_%H%M%S")
+        filename = "VitessceConfig-" + ts + ".json"
+        return filename
+
+    def prepare_choices(self, file_names, file_urls, img_names, img_urls):
+        """ Makes the lists of images and attached files for the form
+        """
+        self.text_choices = [i for i in zip(file_urls, file_names)]
+        self.image_choices = [i for i in zip(img_urls, img_names)]
+
+        self.text_choices.insert(0, ('', '---'))
+        self.image_choices.insert(0, ('', '---'))
+
+        return self.text_choices, self.image_choices