Merge pull request #107 from computational-cell-analytics/more-models-and-samples

Add new sample data and more models

Author: constantinpape

synapse_net/inference/inference.py

@@ -31,6 +31,10 @@ def _get_model_registry():
         "vesicles_2d": "eb0b74f7000a0e6a25b626078e76a9452019f2d1ea6cf2033073656f4f055df1",
         "vesicles_3d": "b329ec1f57f305099c984fbb3d7f6ae4b0ff51ec2fa0fa586df52dad6b84cf29",
         "vesicles_cryo": "782f5a21c3cda82c4e4eaeccc754774d5aaed5929f8496eb018aad7daf91661b",
+        # Additional models that are only available in the CLI, not in the plugin model selection.
+        "vesicles_2d_maus": "01506895df6343fc33ffc9c9eb3f975bf42eb4eaaaf4848bac83b57f1b46e460",
+        "vesicles_3d_endbulb": "8582c7e3e5f16ef2bf34d6f9e34644862ca3c76835c9e7d44475c9dd7891d228",
+        "vesicles_3d_innerear": "924f0f7cfb648a3a6931c1d48d8b1fdc6c0c0d2cb3330fe2cae49d13e7c3b69d",
     }
     urls = {
         "active_zone": "https://owncloud.gwdg.de/index.php/s/zvuY342CyQebPsX/download",
@@ -42,6 +46,10 @@ def _get_model_registry():
         "vesicles_2d": "https://owncloud.gwdg.de/index.php/s/d72QIvdX6LsgXip/download",
         "vesicles_3d": "https://owncloud.gwdg.de/index.php/s/A425mkAOSqePDhx/download",
         "vesicles_cryo": "https://owncloud.gwdg.de/index.php/s/e2lVdxjCJuZkLJm/download",
+        # Additional models that are only available in the CLI, not in the plugin model selection.
+        "vesicles_2d_maus": "https://owncloud.gwdg.de/index.php/s/sZ8woLr0zs5zOpv/download",
+        "vesicles_3d_endbulb": "https://owncloud.gwdg.de/index.php/s/16tmnWrEDpYIMzU/download",
+        "vesicles_3d_innerear": "https://owncloud.gwdg.de/index.php/s/UFUCYivsCxrqISX/download",
     }
     cache_dir = get_cache_dir()
     models = pooch.create(
@@ -108,6 +116,10 @@ def get_model_training_resolution(model_type: str) -> Dict[str, float]:
         "vesicles_2d": {"x": 1.35, "y": 1.35},
         "vesicles_3d": {"x": 1.35, "y": 1.35, "z": 1.35},
         "vesicles_cryo": {"x": 1.35, "y": 1.35, "z": 0.88},
+        # TODO add the correct resolutions, these are the resolutions of the source models.
+        "vesicles_2d_maus": {"x": 1.35, "y": 1.35},
+        "vesicles_3d_endbulb": {"x": 1.35, "y": 1.35, "z": 1.35},
+        "vesicles_3d_innerear": {"x": 1.35, "y": 1.35, "z": 1.35},
     }
     return resolutions[model_type]
 

synapse_net/napari.yaml

@@ -33,6 +33,12 @@ contributions:
     - id: synapse_net.sample_data_tem_tomo
       python_name: synapse_net.sample_data:sample_data_tem_tomo
       title: Load TEM Tomo sample data
+    - id: synapse_net.sample_data_tomo_small
+      python_name: synapse_net.sample_data:sample_data_tomo_small
+      title: Load small tomo sample data
+    - id: synapse_net.sample_data_mito_small
+      python_name: synapse_net.sample_data:sample_data_mito_small
+      title: Load TEM Tomo sample data
 
   readers:
     - command: synapse_net.file_reader
@@ -61,3 +67,9 @@ contributions:
     - command: synapse_net.sample_data_tem_tomo
       display_name: TEM Tomo Sample Data
       key: synapse-net-tem-tomo
+    - command: synapse_net.sample_data_tomo_small
+      display_name: Small Tomo Sample Data
+      key: synapse-net-tomo-small
+    - command: synapse_net.sample_data_mito_small
+      display_name: Small Mito Sample Data
+      key: synapse-net-mito-small

synapse_net/sample_data.py

@@ -17,10 +17,14 @@ def get_sample_data(name: str) -> str:
     registry = {
         "tem_2d.mrc": "3c6f9ff6d7673d9bf2fd46c09750c3c7dbb8fa1aa59dcdb3363b65cc774dcf28",
         "tem_tomo.mrc": "fe862ce7c22000d4440e3aa717ca9920b42260f691e5b2ab64cd61c928693c99",
+        "tomo_small.mrc": "057b214777157682e220958e7ca5c90104eada67210a5589572134ac0d8d177f",
+        "mito_small.mrc": "643534ac080f13a4ba8c9f12f5ea59442cb6d1e7ae1a5aec5ea98b7ae9ab45cc",
     }
     urls = {
         "tem_2d.mrc": "https://owncloud.gwdg.de/index.php/s/5sAQ0U4puAspcHg/download",
         "tem_tomo.mrc": "https://owncloud.gwdg.de/index.php/s/FJDhDfbT4UxhtOn/download",
+        "tomo_small.mrc": "https://owncloud.gwdg.de/index.php/s/03NvEuIye08kkkL/download",
+        "mito_small.mrc": "https://owncloud.gwdg.de/index.php/s/TUhvVMrA7GE8sJv/download",
     }
     key = f"{name}.mrc"
 
@@ -55,6 +59,14 @@ def sample_data_tem_tomo():
     return _sample_data("tem_tomo")
 
 
+def sample_data_tomo_small():
+    return _sample_data("tomo_small")
+
+
+def sample_data_mito_small():
+    return _sample_data("mito_small")
+
+
 def download_data_from_zenodo(path: str, name: str):
     """Download data uploaded for the SynapseNet manuscript from zenodo.
 

synapse_net/tools/segmentation_widget.py

@@ -120,7 +120,12 @@ def load_model_widget(self):
         model_widget = QWidget()
         title_label = QLabel("Select Model:")
 
-        models = ["- choose -"] + list(_get_model_registry().urls.keys())
+        # Exclude the models that are only offered through the CLI and not in the plugin.
+        model_list = set(_get_model_registry().urls.keys())
+        excluded_models = ["vesicles_2d_maus", "vesicles_3d_endbulb", "vesicles_3d_innerear"]
+        model_list = [name for name in model_list if name not in excluded_models]
+
+        models = ["- choose -"] + model_list
         self.model_selector = QComboBox()
         self.model_selector.addItems(models)
         # Create a layout and add the title label and combo box