Merge pull request #24 from AdaptiveMotorControlLab/cy/download-impro…

…vements

Improved pretrained weights usage

napari_cellseg3d/log_utility.py

@@ -1,4 +1,5 @@
 import threading
+import warnings
 
 from qtpy import QtCore
 from qtpy.QtGui import QTextCursor
@@ -28,13 +29,15 @@ def write(self, message):
         try:
             if not hasattr(self, "flag"):
                 self.flag = False
-            message = message.replace('\r', '').rstrip()
+            message = message.replace("\r", "").rstrip()
             if message:
                 method = "replace_last_line" if self.flag else "append"
-                QtCore.QMetaObject.invokeMethod(self,
-                                                method,
-                                                QtCore.Qt.QueuedConnection,
-                                                QtCore.Q_ARG(str, message))
+                QtCore.QMetaObject.invokeMethod(
+                    self,
+                    method,
+                    QtCore.Qt.QueuedConnection,
+                    QtCore.Q_ARG(str, message),
+                )
                 self.flag = True
             else:
                 self.flag = False
@@ -77,3 +80,10 @@ def print_and_log(self, text, printing=True):
             )
         finally:
             self.lock.release()
+
+    def warn(self, warning):
+        self.lock.acquire()
+        try:
+            warnings.warn(warning)
+        finally:
+            self.lock.release()

napari_cellseg3d/model_workers.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 import importlib.util
 from typing import Optional
+import warnings
 
 import numpy as np
 from tifffile import imwrite
@@ -65,19 +66,28 @@
     Path("/models/pretrained")
 )
 
+
 class WeightsDownloader:
+    """A utility class the downloads the weights of a model when needed."""
+
+    def __init__(self, log_widget: Optional[log_utility.Log] = None):
+        """
+        Creates a WeightsDownloader, optionally with a log widget to display the progress.
 
-    def __init__(self, log_widget: Optional[log_utility.Log]= None):
+        Args:
+            log_widget (log_utility.Log): a Log to display the progress bar in. If None, uses print()
+        """
         self.log_widget = log_widget
 
-    def download_weights(self,model_name: str):
+    def download_weights(self, model_name: str, model_weights_filename: str):
         """
-            Downloads a specific pretrained model.
-            This code is adapted from DeepLabCut with permission from MWMathis.
+        Downloads a specific pretrained model.
+        This code is adapted from DeepLabCut with permission from MWMathis.
 
-            Args:
-                model_name (str): name of the model to download
-            """
+        Args:
+            model_name (str): name of the model to download
+            model_weights_filename (str): name of the .pth file expected for the model
+        """
         import json
         import tarfile
         import urllib.request
@@ -94,6 +104,17 @@ def show_progress(count, block_size, total_size):
         json_path = os.path.join(
             pretrained_folder_path, "pretrained_model_urls.json"
         )
+
+        check_path = os.path.join(
+            pretrained_folder_path, model_weights_filename
+        )
+        if os.path.exists(check_path):
+            message = f"Weight file {model_weights_filename} already exists, skipping download step"
+            if self.log_widget is not None:
+                self.log_widget.print_and_log(message, printing=False)
+            print(message)
+            return
+
         with open(json_path) as f:
             neturls = json.load(f)
         if model_name in neturls.keys():
@@ -107,9 +128,16 @@ def show_progress(count, block_size, total_size):
                 pbar = tqdm(unit="B", total=total_size, position=0)
             else:
                 self.log_widget.print_and_log(start_message)
-                pbar = tqdm(unit="B", total=total_size, position=0, file=self.log_widget)
+                pbar = tqdm(
+                    unit="B",
+                    total=total_size,
+                    position=0,
+                    file=self.log_widget,
+                )
 
-            filename, _ = urllib.request.urlretrieve(url, reporthook=show_progress)
+            filename, _ = urllib.request.urlretrieve(
+                url, reporthook=show_progress
+            )
             with tarfile.open(filename, mode="r:gz") as tar:
                 tar.extractall(pretrained_folder_path)
         else:
@@ -121,10 +149,12 @@ def show_progress(count, block_size, total_size):
 class LogSignal(WorkerBaseSignals):
     """Signal to send messages to be logged from another thread.
 
-    Separate from Worker instances as indicated `here`_"""
+    Separate from Worker instances as indicated `here`_"""  # TODO link ?
 
     log_signal = Signal(str)
     """qtpy.QtCore.Signal: signal to be sent when some text should be logged"""
+    warn_signal = Signal(str)
+    """qtpy.QtCore.Signal: signal to be sent when some warning should be emitted in main thread"""
 
     # Should not be an instance variable but a class variable, not defined in __init__, see
     # https://stackoverflow.com/questions/2970312/pyqt4-qtcore-pyqtsignal-object-has-no-attribute-connect
@@ -185,6 +215,7 @@ def __init__(
         super().__init__(self.inference)
         self._signals = LogSignal()  # add custom signals
         self.log_signal = self._signals.log_signal
+        self.warn_signal = self._signals.warn_signal
         ###########################################
         ###########################################
         self.device = device
@@ -204,7 +235,6 @@ def __init__(
         self.downloader = WeightsDownloader()
         """Download utility"""
 
-
     @staticmethod
     def create_inference_dict(images_filepaths):
         """Create a dict for MONAI with "image" keys with all image paths in :py:attr:`~self.images_filepaths`
@@ -225,6 +255,10 @@ def log(self, text):
         """
         self.log_signal.emit(text)
 
+    def warn(self, warning):
+        """Sends a warning to main thread"""
+        self.warn_signal.emit(warning)
+
     def log_parameters(self):
 
         self.log("-" * 20)
@@ -297,7 +331,7 @@ def inference(self):
         sys = platform.system()
         print(f"OS is {sys}")
         if sys == "Darwin":
-            torch.set_num_threads(1) # required for threading on macOS ?
+            torch.set_num_threads(1)  # required for threading on macOS ?
             self.log("Number of threads has been set to 1 for macOS")
 
         images_dict = self.create_inference_dict(self.images_filepaths)
@@ -323,7 +357,11 @@ def inference(self):
         model = self.model_dict["class"].get_net()
         if self.model_dict["name"] == "SegResNet":
             model = self.model_dict["class"].get_net()(
-                input_image_size=[dims, dims, dims],  # TODO FIX ! find a better way & remove model-specific code
+                input_image_size=[
+                    dims,
+                    dims,
+                    dims,
+                ],  # TODO FIX ! find a better way & remove model-specific code
                 out_channels=1,
                 # dropout_prob=0.3,
             )
@@ -372,8 +410,13 @@ def inference(self):
         if self.weights_dict["custom"]:
             weights = self.weights_dict["path"]
         else:
-            self.downloader.download_weights(self.model_dict["name"])
-            weights = os.path.join(WEIGHTS_DIR, self.model_dict["class"].get_weights_file())
+            self.downloader.download_weights(
+                self.model_dict["name"],
+                self.model_dict["class"].get_weights_file(),
+            )
+            weights = os.path.join(
+                WEIGHTS_DIR, self.model_dict["class"].get_weights_file()
+            )
 
         model.load_state_dict(
             torch.load(
@@ -611,7 +654,10 @@ def __init__(
         super().__init__(self.train)
         self._signals = LogSignal()
         self.log_signal = self._signals.log_signal
+        self.warn_signal = self._signals.warn_signal
 
+        self._weight_error = False
+        #############################################
         self.device = device
         self.model_dict = model_dict
         self.weights_path = weights_path
@@ -633,7 +679,7 @@ def __init__(
 
         self.train_files = []
         self.val_files = []
-
+        #######################################
         self.downloader = WeightsDownloader()
 
     def set_download_log(self, widget):
@@ -647,6 +693,10 @@ def log(self, text):
         """
         self.log_signal.emit(text)
 
+    def warn(self, warning):
+        """Sends a warning to main thread"""
+        self.warn_signal.emit(warning)
+
     def log_parameters(self):
 
         self.log("-" * 20)
@@ -690,6 +740,13 @@ def log_parameters(self):
 
         if self.weights_path is not None:
             self.log(f"Using weights from : {self.weights_path}")
+            if self._weight_error:
+                self.log(
+                    ">>>>>>>>>>>>>>>>>\n"
+                    "WARNING:\nChosen weights were incompatible with the model,\n"
+                    "the model will be trained from random weights\n"
+                    "<<<<<<<<<<<<<<<<<\n"
+                )
 
         # self.log("\n")
         self.log("-" * 20)
@@ -904,18 +961,27 @@ def train(self):
         if self.weights_path is not None:
             if self.weights_path == "use_pretrained":
                 weights_file = model_class.get_weights_file()
-                self.downloader.download_weights(model_name)
+                self.downloader.download_weights(model_name, weights_file)
                 weights = os.path.join(WEIGHTS_DIR, weights_file)
                 self.weights_path = weights
             else:
                 weights = os.path.join(self.weights_path)
 
-            model.load_state_dict(
-                torch.load(
-                    weights,
-                    map_location=self.device,
+            try:
+                model.load_state_dict(
+                    torch.load(
+                        weights,
+                        map_location=self.device,
+                    )
                 )
-            )
+            except RuntimeError:
+                warn = (
+                    "WARNING:\nIt seems the weights were incompatible with the model,\n"
+                    "the model will be trained from random weights"
+                )
+                self.log(warn)
+                self.warn(warn)
+                self._weight_error = True
 
         if self.device.type == "cuda":
             self.log("\nUsing GPU :")

napari_cellseg3d/models/model_SegResNet.py

@@ -1,7 +1,6 @@
 from monai.networks.nets import SegResNetVAE
 
 
-
 def get_net():
     return SegResNetVAE
 

napari_cellseg3d/models/model_TRAILMAP.py

@@ -2,12 +2,12 @@
 from torch import nn
 
 
-
 def get_weights_file():
     # model additionally trained on Mathis/Wyss mesoSPIM data
     return "TRAILMAP.pth"
     # FIXME currently incorrect, find good weights from TRAILMAP_test and upload them
 
+
 def get_net():
     return TRAILMAP(1, 1)
 
@@ -120,4 +120,3 @@ def outBlock(self, in_ch, out_ch, kernel_size, padding="same"):
             # nn.BatchNorm3d(out_ch),
         )
         return out
-

napari_cellseg3d/models/model_VNet.py

@@ -2,7 +2,6 @@
 from monai.networks.nets import VNet
 
 
-
 def get_net():
     return VNet()
 

napari_cellseg3d/plugin_model_inference.py

@@ -599,6 +599,7 @@ def start(self):
 
             self.worker.started.connect(self.on_start)
             self.worker.log_signal.connect(self.log.print_and_log)
+            self.worker.warn_signal.connect(self.log.warn)
             self.worker.yielded.connect(yield_connect_show_res)
             self.worker.errored.connect(
                 yield_connect_show_res

napari_cellseg3d/plugin_model_training.py

@@ -857,6 +857,7 @@ def start(self):
             [btn.setVisible(False) for btn in self.close_buttons]
 
             self.worker.log_signal.connect(self.log.print_and_log)
+            self.worker.warn_signal.connect(self.log.warn)
 
             self.worker.started.connect(self.on_start)
 
@@ -994,7 +995,7 @@ def make_csv(self):
         if len(self.loss_values) == 0 or self.loss_values is None:
             warnings.warn("No loss values to add to csv !")
             return
-        
+
         self.df = pd.DataFrame(
             {
                 "epoch": size_column,

napari_cellseg3d/utils.py

@@ -978,5 +978,3 @@ def merge_imgs(imgs, original_image_shape):
 
     print(merged_imgs.shape)
     return merged_imgs
-
-