Merge pull request #105 from PytorchConnectomics/leander/incorporate-user-feedback

Incorporate User Feedback from the Case and User Studies

Author: Lauenburg

.gitignore

@@ -53,5 +53,6 @@ datasets/
 flask_session
 synAnno.json
 secrets/
+tmp/
 
 .vscode/

README.md

@@ -1,5 +1,10 @@
 # SynAnno
 
+## Live Demo
+A demo is available [here](http://16.170.214.77/)
+
+## Table of Contents
+
 SynAnno is a tool designed for proofreading and correcting synaptic polarity annotation from electron microscopy (EM) volumes - specifically the [H01](https://h01-release.storage.googleapis.com/landing.html) dataset. SynAnno is aimed for integration with CAVE (Connectome Annotation Versioning Engine).
 
 - [Key Components and Subjects](#key-components-and-subjects)

synanno/__init__.py

@@ -85,7 +85,7 @@ def initialize_global_variables(app):
     app.source = None
     app.cz1, app.cz2, app.cz, app.cy, app.cx = 0, 0, 0, 0, 0
     app.n_pages = 0
-    app.per_page = 24  # Number of images per page
+    app.tiles_per_page = 24  # Number of images per page
     # Neuron skeleton info/data
     app.sections = None
     app.neuron_ready = None

synanno/backend/processing.py

@@ -787,22 +787,24 @@ def calculate_number_of_pages(n_images: int) -> int:
 
     Args:
         n_images: Total number of images.
-        per_page: Number of images per page.
+        tiles_per_page: Number of images per page.
 
     Returns:
         Number of pages.
     """
-    number_pages = n_images // current_app.per_page
-    if n_images % current_app.per_page != 0:
+    number_pages = n_images // current_app.tiles_per_page
+    if n_images % current_app.tiles_per_page != 0:
         number_pages += 1
 
     current_app.synapse_data["page"] = -1  # Initialize pages to -1
 
     # assign pages to synapses
-    for i, start_idx in enumerate(range(0, n_images, current_app.per_page), start=1):
+    for i, start_idx in enumerate(
+        range(0, n_images, current_app.tiles_per_page), start=1
+    ):
         current_app.synapse_data.loc[
             current_app.synapse_data.iloc[
-                start_idx : start_idx + current_app.per_page  # noqa: E203
+                start_idx : start_idx + current_app.tiles_per_page  # noqa: E203
             ].index,
             "page",
         ] = i
@@ -816,7 +818,7 @@ def calculate_number_of_pages_for_neuron_section_based_loading():
 
     This function:
     - Groups synapses by `section_index`.
-    - Assigns page numbers within each section based on `current_app.per_page`.
+    - Assigns page numbers within each section based on `current_app.tiles_per_page`.
     - Adds an extra empty page per section.
 
     Returns:
@@ -839,11 +841,11 @@ def calculate_number_of_pages_for_neuron_section_based_loading():
 
             # Assign pages to synapses within the section
             for i, start_idx in enumerate(
-                range(0, total_synapses, current_app.per_page), start=1
+                range(0, total_synapses, current_app.tiles_per_page), start=1
             ):
                 current_app.synapse_data.loc[
                     synapse_group.iloc[
-                        start_idx : start_idx + current_app.per_page  # noqa: E203
+                        start_idx : start_idx + current_app.tiles_per_page  # noqa: E203
                     ].index,
                     "page",
                 ] = (
@@ -856,7 +858,7 @@ def calculate_number_of_pages_for_neuron_section_based_loading():
                 )
 
             # Increment by the number of pages needed
-            number_of_pages += int(np.ceil(total_synapses / current_app.per_page))
+            number_of_pages += int(np.ceil(total_synapses / current_app.tiles_per_page))
 
         # Add one empty page for the section
         number_of_pages += 1

synanno/routes/false_negatives.py

@@ -122,10 +122,12 @@ def create_new_item(request) -> dict:
     if current_page > -1:
         item["Page"] = current_page
     else:
-        if not (len(current_app.df_metadata) % current_app.per_page == 0):
-            item["Page"] = len(current_app.df_metadata) // current_app.per_page + 1
+        if not (len(current_app.df_metadata) % current_app.tiles_per_page == 0):
+            item["Page"] = (
+                len(current_app.df_metadata) // current_app.tiles_per_page + 1
+            )
         else:
-            item["Page"] = len(current_app.df_metadata) // current_app.per_page
+            item["Page"] = len(current_app.df_metadata) // current_app.tiles_per_page
 
     coordinate_order = list(current_app.coordinate_order.keys())
 

synanno/routes/finish.py

@@ -3,6 +3,7 @@
 import json
 import logging
 import zipfile
+from typing import Optional
 
 from flask import (
     Blueprint,
@@ -131,7 +132,7 @@ def create_zip_with_masks() -> io.BytesIO:
     return zip_buffer
 
 
-def get_metadata_for_image_index(img_index: str) -> dict | None:
+def get_metadata_for_image_index(img_index: str) -> Optional[dict]:
     """Retrieve metadata for a given image index."""
     img_index_int = int(img_index)  # noqa: F841
     if current_app.df_metadata.query("Image_Index == @img_index_int").to_dict(

synanno/routes/manual_annotate.py

@@ -79,7 +79,7 @@ def save_canvas() -> dict:
     image = decode_image(request.form["imageBase64"])
     page = int(request.form["page"])
     index = int(request.form["data_id"])
-    viewed_instance_slice = int(request.form["viewed_instance_slice"])
+    viewed_instance_slice = int(request.form["viewedInstanceSlice"])
     canvas_type = str(request.form["canvas_type"])
 
     crop_axes = (

synanno/routes/opendata.py

@@ -374,6 +374,8 @@ def upload_file():
     """
     current_app.view_style = request.form.get("view_style")
 
+    current_app.tiles_per_page = int(request.form.get("tiles_per_page"))
+
     save_coordinate_order_and_crop_size(request.form)
 
     source_url = request.form.get("source_url")

synanno/static/annotation_module.js

@@ -46,6 +46,7 @@ $(document).ready(function () {
   });
 
   $('[data-bs-target="#neuroModel"]').on('click', function () {
+    $('#synapse-id-annotation').text(dataId);
     toggleInert($detailsModal, true);
     $neuroModel.modal('show');
   });
@@ -120,6 +121,13 @@ $(document).ready(function () {
     isModalScrollingLocked = true;
 
     const newSlice = currentSlice + (event.originalEvent.deltaY > 0 ? 1 : -1);
+
+    // Restrict scrolling beyond available slices
+    if (newSlice < dataJson.Min_Slice || newSlice > dataJson.Max_Slice) {
+      isModalScrollingLocked = false;
+      return;
+    }
+
     try {
       const exists = await $.get(dataJson.Error_Description === "False Negative" ?
         `/source_img_exists/${dataId}/${newSlice}` :

synanno/static/css/style.css

@@ -1,40 +1,32 @@
 #base-content-container {
-  max-height: 80vh;
+  max-height: 100vh;
   max-width: 100vw;
 }
 
 #image-tile-container {
-  max-height: 70vh;
-  max-width: 70vw;
-}
-
-.correct {
-  background: #abebc6;
+  min-width: 60vw;
+  width: fit-content;
+  margin: 0 auto;
 }
 
 .annotate-item {
-  width: 16.5%;
   text-align: center;
 }
 
-.card>.correct {
+.correct,
+.card > .correct {
   background: #abebc6;
 }
 
-.incorrect {
-  background: #f08080;
-}
 
+.incorrect,
 .card>.incorrect {
   background: #f08080;
 }
 
-.unsure {
-  background: #d7dbdd;
-}
-
+.unsure,
 .card>.unsure {
-  background: #d7dbdd;
+  background: #f6f699;
 }
 
 .card {
@@ -47,13 +39,13 @@
 }
 
 .legend {
-  position: sticky;
-  top: 0;
-  z-index: 900;
+  width: 100%;
+  flex-wrap: wrap;
   display: flex;
   gap: 1rem;
   background-color: white;
-  padding: 1rem;
+  padding: 0.5rem;
+  box-sizing: border-box;
 }
 
 .legend-item {
@@ -71,10 +63,7 @@
 .card-body-proof-read {
   max-height: 23%;
   max-width: 23%;
-  margin-left: 1%;
-  margin-right: 1%;
-  margin-top: 0.5%;
-  margin-bottom: 0.5%;
+  margin: 0.5% 1%;
 }
 
 .card-block>.main-image-categorize>.img_categorize {
@@ -94,8 +83,11 @@
 
 .outsideWrapper {
   margin: auto;
-  width: 384px;
-  height: 384px;
+  width: 452px;
+  height: 452px;
+  background-color: #fff;
+  border-radius: 12px;
+  overflow: hidden;
 }
 
 .insideWrapper {
@@ -108,8 +100,8 @@
   width: 100%;
   height: 100%;
   position: absolute;
-  top: 0px;
-  left: 0px;
+  top: 0;
+  left: 0;
   pointer-events: none;
   z-index: 0;
 }
@@ -122,6 +114,60 @@
   left: 0;
 }
 
+/* drawing modal content */
+.modal-content {
+  background: #ffffff;
+  border-radius: 1rem;
+  padding: 0.5rem;
+  border: none;
+  box-shadow: 0 4px 20px rgba(0, 0, 0, 0.1);
+}
+
+.modal-dialog {
+  border: none !important;
+  box-shadow: none !important;
+}
+
+.modal-header,
+.card-header {
+  background: #f8f9fa;
+  border-bottom: none !important;
+  border-top-left-radius: 1rem;
+  border-top-right-radius: 1rem;
+  border-bottom-left-radius: 0.5rem;
+  border-bottom-right-radius: 0.5rem;
+  box-shadow: none;
+}
+
+.btn {
+  transition: all 0.2s ease-in-out;
+}
+
+.btn:hover {
+  transform: translateY(-1px);
+  box-shadow: 0 4px 8px rgba(0, 0, 0, 0.1);
+}
+
+.modal-footer {
+  padding: 0rem 1rem;
+  max-height: 40px;
+  border-top: none;
+}
+
+#centralBadge {
+  z-index: 1; /* Ensure it's above the image, but below the modal header */
+  pointer-events: none; /* Prevent interaction issues */
+  font-size: 0.75rem;
+  opacity: 0.7;
+}
+
+#neuron-id-draw .badge.disabled {
+  opacity: 0.8;
+  cursor: default;
+  pointer-events: none;
+  padding: 10px;
+}
+
 /* css for the open data form */
 .syn-id-container {
   display: flex;
@@ -182,11 +228,11 @@
   /* Initially hidden */
   position: relative;
   /* Default inside flex container */
-  width: 33vw;
+  width: 40vw;
   /* Always take 33% of the screen width */
-  height: 90vh;
+  height: 91vh;
   /* Always take 80% of the screen height */
-  margin-top: 5px;
+  margin-top: 4px;
   background: #fff;
   border: 1px solid #ccc;
   box-shadow: 2px 2px 10px rgba(0, 0, 0, 0.2);
@@ -278,3 +324,17 @@
 .toggle-btn:hover {
   background: #888;
 }
+
+.metadata-overlay {
+  position: absolute;
+  top: 5px;
+  right: 5px;
+  background: rgba(0, 0, 0, 0.55);
+  color: white;
+  font-size: 0.65rem;
+  padding: 2px 4px;
+  border-radius: 3px;
+  z-index: 2;
+  font-family: monospace;
+  pointer-events: none;
+}