Cosem starter - Head matching

dacapo/experiments/run.py

@@ -59,8 +59,14 @@ def __init__(self, run_config):
             if run_config.start_config is not None
             else None
         )
-        if self.start is not None:
-            self.start.initialize_weights(self.model)
+        if self.start is None:
+            return
+        else:
+            if hasattr(run_config.task_config,"channels"):
+                new_head = run_config.task_config.channels
+            else:
+                new_head = None
+            self.start.initialize_weights(self.model,new_head=new_head)
 
     @staticmethod
     def get_validation_scores(run_config) -> ValidationScores:

dacapo/experiments/starts/cosem_start.py

@@ -2,15 +2,39 @@
 import logging
 from cellmap_models import cosem
 from pathlib import Path
-from .start import Start
+from .start import Start, _set_weights
 
 logger = logging.getLogger(__file__)
 
-
+def get_model_setup(run):
+    try:
+        model = cosem.load_model(run)
+        if hasattr(model, "classes_channels"):
+            classes_channels =  model.classes_channels
+        else:
+            classes_channels = None
+        if hasattr(model, "voxel_size_input"):
+            voxel_size_input = model.voxel_size_input
+        else:
+            voxel_size_input = None
+        if hasattr(model, "voxel_size_output"):
+            voxel_size_output = model.voxel_size_output
+        else:
+            voxel_size_output = None
+        return classes_channels, voxel_size_input, voxel_size_output
+    except Exception as e:
+        logger.error(f"could not load model setup: {e} - Not a big deal, model will train wiithout head matching")
+        return None, None, None
+
 class CosemStart(Start):
     def __init__(self, start_config):
-        super().__init__(start_config)
+        self.run = start_config.run
+        self.criterion = start_config.criterion
         self.name = f"{self.run}/{self.criterion}"
+        channels, voxel_size_input, voxel_size_output = get_model_setup(self.run)
+        if voxel_size_input is not None:
+            logger.warning(f"Starter model resolution: input {voxel_size_input} output {voxel_size_output}, Make sure to set the correct resolution for the input data.")
+        self.channels = channels
 
     def check(self):
         from dacapo.store.create_store import create_weights_store
@@ -25,7 +49,8 @@ def check(self):
         else:
             logger.info(f"Checkpoint for {self.name} exists.")
 
-    def initialize_weights(self, model):
+    def initialize_weights(self, model, new_head=None):
+        self.check()
         from dacapo.store.create_store import create_weights_store
 
         weights_store = create_weights_store()
@@ -36,4 +61,6 @@ def initialize_weights(self, model):
             path = weights_dir / self.criterion
             cosem.download_checkpoint(self.name, path)
         weights = weights_store._retrieve_weights(self.run, self.criterion)
-        super._set_weights(model, weights)
+        _set_weights(model, weights, self.run, self.criterion, self.channels, new_head)
+
+

dacapo/experiments/starts/start.py

@@ -3,6 +3,60 @@
 
 logger = logging.getLogger(__file__)
 
+head_keys = ["prediction_head.weight","prediction_head.bias","chain.1.weight","chain.1.bias"]
+
+def match_heads(model, head_weights, old_head, new_head ):
+    for label in new_head:
+        if label in old_head:
+            logger.warning(f"matching head for {label}.")
+            old_index = old_head.index(label)
+            new_index = new_head.index(label)
+            for key in head_keys:
+                if key in model.state_dict().keys():
+                    n_val = head_weights[key][old_index]
+                    model.state_dict()[key][new_index] = n_val
+            logger.warning(f"matched head for {label}.")
+
+def _set_weights(model, weights, run, criterion, old_head=None, new_head=None):
+    logger.warning(f"loading weights from run {run}, criterion: {criterion}, old_head {old_head}, new_head: {new_head}")
+    try:
+        if old_head and new_head:
+            try:
+                logger.warning(f"matching heads from run {run}, criterion: {criterion}")
+                logger.warning(f"old head: {old_head}")
+                logger.warning(f"new head: {new_head}")
+                head_weights = {}
+                for key in head_keys:
+                    head_weights[key] = weights.model[key]
+                for key in head_keys:
+                    weights.model.pop(key, None)
+                model.load_state_dict(weights.model, strict=False)
+                model = match_heads(model, head_weights, old_head, new_head)
+            except RuntimeError as e:
+                logger.error(f"ERROR starter matching head: {e}")
+                logger.warning(f"removing head from run {run}, criterion: {criterion}")
+                for key in head_keys:
+                    weights.model.pop(key, None)
+                model.load_state_dict(weights.model, strict=False)
+                logger.warning(f"loaded weights in non strict mode from run {run}, criterion: {criterion}")
+        else:
+            try:
+                model.load_state_dict(weights.model)
+            except RuntimeError as e:
+                logger.warning(e)
+                model_dict = model.state_dict()
+                pretrained_dict = {
+                    k: v
+                    for k, v in weights.model.items()
+                    if k in model_dict and v.size() == model_dict[k].size()
+                }
+                model_dict.update(
+                    pretrained_dict
+                ) 
+                model.load_state_dict(model_dict)
+                logger.warning(f"loaded only common layers from weights")
+    except RuntimeError as e:
+        logger.warning(f"ERROR starter: {e}")
 
 class Start(ABC):
     """
@@ -32,28 +86,12 @@ def __init__(self, start_config):
         self.run = start_config.run
         self.criterion = start_config.criterion
 
-    def _set_weights(self, model, weights):
-        print(f"loading weights from run {self.run}, criterion: {self.criterion}")
-        # load the model weights (taken from torch load_state_dict source)
-        try:
-            model.load_state_dict(weights.model)
-        except RuntimeError as e:
-            logger.warning(e)
-            # if the model is not the same, we can try to load the weights
-            # of the common layers
-            model_dict = model.state_dict()
-            pretrained_dict = {
-                k: v
-                for k, v in weights.model.items()
-                if k in model_dict and v.size() == model_dict[k].size()
-            }
-            model_dict.update(
-                pretrained_dict
-            )  # update only the existing and matching layers
-            model.load_state_dict(model_dict)
-            logger.warning(f"loaded only common layers from weights")
+        if hasattr(start_config.task_config,"channels"):
+            self.channels = start_config.task_config.channels
+        else:
+            self.channels = None        
 
-    def initialize_weights(self, model):
+    def initialize_weights(self, model,new_head=None):
         """
         Retrieves the weights from the dacapo store and load them into
         the model.
@@ -72,4 +110,5 @@ def initialize_weights(self, model):
 
         weights_store = create_weights_store()
         weights = weights_store._retrieve_weights(self.run, self.criterion)
-        self._set_weights(model, weights)
+        _set_weights(model, weights, self.run, self.criterion, self.channels, new_head)
+

dacapo/store/conversion_hooks.py

@@ -21,6 +21,7 @@ def register_hierarchy_hooks(converter):
     """Central place to register type hierarchies for conversion."""
 
     converter.register_hierarchy(TaskConfig, cls_fun)
+    converter.register_hierarchy(StartConfig, cls_fun)
     converter.register_hierarchy(ArchitectureConfig, cls_fun)
     converter.register_hierarchy(TrainerConfig, cls_fun)
     converter.register_hierarchy(AugmentConfig, cls_fun)