cellfinder 1.2.0__py3-none-any.whl → 1.3.0rc0__py3-none-any.whl

cellfinder/core/tools/prep.py

@@ -9,9 +9,7 @@ from pathlib import Path
 from typing import Optional
 
 from brainglobe_utils.general.config import get_config_obj
-from brainglobe_utils.general.system import get_num_processes
 
-import cellfinder.core.tools.tf as tf_tools
 from cellfinder.core import logger
 from cellfinder.core.download.download import (
     DEFAULT_DOWNLOAD_DIRECTORY,
@@ -26,20 +24,13 @@ def prep_model_weights(
     model_weights: Optional[os.PathLike],
     install_path: Optional[os.PathLike],
     model_name: model_type,
-    n_free_cpus: int,
 ) -> Path:
-    n_processes = get_num_processes(min_free_cpu_cores=n_free_cpus)
-    prep_tensorflow(n_processes)
+    # prepare models (get default weights or provided ones)
     model_weights = prep_models(model_weights, install_path, model_name)
 
     return model_weights
 
 
-def prep_tensorflow(max_threads: int) -> None:
-    tf_tools.set_tf_threads(max_threads)
-    tf_tools.allow_gpu_memory_growth()
-
-
 def prep_models(
     model_weights_path: Optional[os.PathLike],
     install_path: Optional[os.PathLike],

cellfinder/core/train/train_yml.py

@@ -22,7 +22,10 @@ from brainglobe_utils.general.numerical import (
     check_positive_float,
     check_positive_int,
 )
-from brainglobe_utils.general.system import ensure_directory_exists
+from brainglobe_utils.general.system import (
+    ensure_directory_exists,
+    get_num_processes,
+)
 from brainglobe_utils.IO.cells import find_relevant_tiffs
 from brainglobe_utils.IO.yaml import read_yaml_section
 from fancylog import fancylog
@@ -33,11 +36,6 @@ from cellfinder.core import logger
 from cellfinder.core.classify.resnet import layer_type
 from cellfinder.core.download.download import DEFAULT_DOWNLOAD_DIRECTORY
 
-tf_suppress_log_messages = [
-    "sample_weight modes were coerced from",
-    "multiprocessing can interact badly with TensorFlow",
-]
-
 depth_type = Literal["18", "34", "50", "101", "152"]
 
 models: Dict[depth_type, layer_type] = {
@@ -318,11 +316,7 @@ def run(
     save_progress=False,
     epochs=100,
 ):
-    from cellfinder.core.main import suppress_tf_logging
-
-    suppress_tf_logging(tf_suppress_log_messages)
-
-    from tensorflow.keras.callbacks import (
+    from keras.callbacks import (
         CSVLogger,
         ModelCheckpoint,
         TensorBoard,
@@ -339,7 +333,6 @@ def run(
         model_weights=model_weights,
         install_path=install_path,
         model_name=model,
-        n_free_cpus=n_free_cpus,
     )
 
     yaml_contents = parse_yaml(yaml_file)
@@ -361,6 +354,7 @@ def run(
 
     signal_train, background_train, labels_train = make_lists(tiff_files)
 
+    n_processes = get_num_processes(min_free_cpu_cores=n_free_cpus)
     if test_fraction > 0:
         logger.info("Splitting data into training and validation datasets")
         (
@@ -387,15 +381,17 @@ def run(
             labels=labels_test,
             batch_size=batch_size,
             train=True,
+            use_multiprocessing=False,
+            workers=n_processes,
         )
 
         # for saving checkpoints
-        base_checkpoint_file_name = "-epoch.{epoch:02d}-loss-{val_loss:.3f}.h5"
+        base_checkpoint_file_name = "-epoch.{epoch:02d}-loss-{val_loss:.3f}"
 
     else:
         logger.info("No validation data selected.")
         validation_generator = None
-        base_checkpoint_file_name = "-epoch.{epoch:02d}.h5"
+        base_checkpoint_file_name = "-epoch.{epoch:02d}"
 
     training_generator = CubeGeneratorFromDisk(
         signal_train,
@@ -405,6 +401,8 @@ def run(
         shuffle=True,
         train=True,
         augment=not no_augment,
+        use_multiprocessing=False,
+        workers=n_processes,
     )
     callbacks = []
 
@@ -421,9 +419,14 @@ def run(
 
     if not no_save_checkpoints:
         if save_weights:
-            filepath = str(output_dir / ("weight" + base_checkpoint_file_name))
+            filepath = str(
+                output_dir
+                / ("weight" + base_checkpoint_file_name + ".weights.h5")
+            )
         else:
-            filepath = str(output_dir / ("model" + base_checkpoint_file_name))
+            filepath = str(
+                output_dir / ("model" + base_checkpoint_file_name + ".keras")
+            )
 
         checkpoints = ModelCheckpoint(
             filepath,
@@ -432,25 +435,26 @@ def run(
         callbacks.append(checkpoints)
 
     if save_progress:
-        filepath = str(output_dir / "training.csv")
-        csv_logger = CSVLogger(filepath)
+        csv_filepath = str(output_dir / "training.csv")
+        csv_logger = CSVLogger(csv_filepath)
         callbacks.append(csv_logger)
 
     logger.info("Beginning training.")
+    # Keras 3.0: `use_multiprocessing` input is set in the
+    # `training_generator` (False by default)
     model.fit(
         training_generator,
         validation_data=validation_generator,
-        use_multiprocessing=False,
         epochs=epochs,
         callbacks=callbacks,
     )
 
     if save_weights:
         logger.info("Saving model weights")
-        model.save_weights(str(output_dir / "model_weights.h5"))
+        model.save_weights(output_dir / "model.weights.h5")
     else:
         logger.info("Saving model")
-        model.save(output_dir / "model.h5")
+        model.save(output_dir / "model.keras")
 
     logger.info(
         "Finished training, " "Total time taken: %s",

{cellfinder-1.2.0.dist-info → cellfinder-1.3.0rc0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.2.0
+Version: 1.3.0rc0
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -31,10 +31,10 @@ Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
+Requires-Dist: keras >=3.0.0
+Requires-Dist: torch >=2.1.0
 Requires-Dist: tifffile
 Requires-Dist: tqdm
-Requires-Dist: tensorflow <2.12.0,>=2.5.0 ; platform_system != "Darwin" or platform_machine != "arm64"
-Requires-Dist: tensorflow-macos <2.12.0,>=2.5.0 ; platform_system == "Darwin" and platform_machine == "arm64"
 Provides-Extra: dev
 Requires-Dist: black ; extra == 'dev'
 Requires-Dist: pre-commit ; extra == 'dev'

cellfinder-1.3.0rc0.dist-info/RECORD

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cellfinder/core/tools/tf.py

@@ -1,46 +0,0 @@
-import tensorflow as tf
-
-from cellfinder.core import logger
-
-
-def allow_gpu_memory_growth():
-    """
-    If a gpu is present, prevent tensorflow from using all the memory straight
-    away. Allows multiple processes to use the GPU (and avoid occasional
-    errors on some systems) at the cost of a slight performance penalty.
-    """
-    gpus = tf.config.experimental.list_physical_devices("GPU")
-    if gpus:
-        logger.debug("Allowing GPU memory growth")
-        try:
-            # Currently, memory growth needs to be the same across GPUs
-            for gpu in gpus:
-                tf.config.experimental.set_memory_growth(gpu, True)
-            logical_gpus = tf.config.experimental.list_logical_devices("GPU")
-            logger.debug(
-                f"{len(gpus)} physical GPUs, {len(logical_gpus)} logical GPUs"
-            )
-        except RuntimeError as e:
-            # Memory growth must be set before GPUs have been initialized
-            print(e)
-    else:
-        logger.debug("No GPUs found, using CPU.")
-
-
-def set_tf_threads(max_threads):
-    """
-    Limit the number of threads that tensorflow uses
-    :param max_threads: Maximum number of threads to use
-    :return:
-    """
-    logger.debug(
-        f"Setting maximum number of threads for tensorflow "
-        f"to: {max_threads}"
-    )
-
-    # If statements are for testing. If tf is initialised, then setting these
-    # parameters throws an error
-    if tf.config.threading.get_inter_op_parallelism_threads() != 0:
-        tf.config.threading.set_inter_op_parallelism_threads(max_threads)
-    if tf.config.threading.get_intra_op_parallelism_threads() != 0:
-        tf.config.threading.set_intra_op_parallelism_threads(max_threads)