From c7be35285361bdcd9377c46ecd02efa7e42e2fb6 Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Fri, 26 Apr 2024 12:57:15 +0200
Subject: [PATCH] [train] move balance-classes option to classification script
only
---
src/mednet/libs/classification/scripts/train.py | 13 ++++++++++++-
src/mednet/libs/common/scripts/train.py | 15 ++-------------
src/mednet/libs/segmentation/models/lwnet.py | 4 ++--
src/mednet/libs/segmentation/scripts/train.py | 4 +---
4 files changed, 17 insertions(+), 19 deletions(-)
diff --git a/src/mednet/libs/classification/scripts/train.py b/src/mednet/libs/classification/scripts/train.py
index dbc14ebe..6e1e28e8 100644
--- a/src/mednet/libs/classification/scripts/train.py
+++ b/src/mednet/libs/classification/scripts/train.py
@@ -27,6 +27,17 @@ logger = setup("mednet", format="%(levelname)s: %(message)s")
""",
)
@reusable_options
+@click.option(
+ "--balance-classes/--no-balance-classes",
+ "-B/-N",
+ help="""If set, balances weights of the random sampler during
+ training so that samples from all sample classes are picked
+ equitably.""",
+ required=True,
+ show_default=True,
+ default=True,
+ cls=ResourceOption,
+)
@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
def train(
model,
@@ -104,7 +115,7 @@ def train(
seed,
parallel,
monitoring_interval,
- balance_classes,
+ balance_classes=balance_classes,
)
run(
diff --git a/src/mednet/libs/common/scripts/train.py b/src/mednet/libs/common/scripts/train.py
index 32d7bd94..db48174d 100644
--- a/src/mednet/libs/common/scripts/train.py
+++ b/src/mednet/libs/common/scripts/train.py
@@ -197,17 +197,6 @@ def reusable_options(f):
default=5.0,
cls=ResourceOption,
)
- @click.option(
- "--balance-classes/--no-balance-classes",
- "-B/-N",
- help="""If set, balances weights of the random sampler during
- training so that samples from all sample classes are picked
- equitably.""",
- required=True,
- show_default=True,
- default=True,
- cls=ResourceOption,
- )
@functools.wraps(f)
def wrapper_reusable_options(*args, **kwargs):
return f(*args, **kwargs)
@@ -317,7 +306,7 @@ def save_json_data(
seed,
parallel,
monitoring_interval,
- balance_classes,
+ **kwargs,
) -> None: # numpydoc ignore=PR01
"""Save training hyperparameters into a .json file."""
from .utils import (
@@ -342,10 +331,10 @@ def save_json_data(
seed=seed,
parallel=parallel,
monitoring_interval=monitoring_interval,
- balance_classes=balance_classes,
model_name=model.name,
),
)
+ json_data.update(kwargs)
json_data.update(model_summary(model))
json_data = {k.replace("_", "-"): v for k, v in json_data.items()}
save_json_with_backup(output_folder / "meta.json", json_data)
diff --git a/src/mednet/libs/segmentation/models/lwnet.py b/src/mednet/libs/segmentation/models/lwnet.py
index ac23d617..c3190f0b 100644
--- a/src/mednet/libs/segmentation/models/lwnet.py
+++ b/src/mednet/libs/segmentation/models/lwnet.py
@@ -303,7 +303,7 @@ class LittleWNet(Model):
def training_step(self, batch, batch_idx):
images = batch[0]
- ground_truths = batch[1]["label"]
+ ground_truths = batch[1]["target"]
masks = torch.ones_like(ground_truths) if len(batch) < 4 else batch[3]
outputs = self(self._augmentation_transforms(images))
@@ -312,7 +312,7 @@ class LittleWNet(Model):
def validation_step(self, batch, batch_idx):
images = batch[0]
- ground_truths = batch[1]["label"]
+ ground_truths = batch[1]["target"]
masks = torch.ones_like(ground_truths) if len(batch) < 4 else batch[3]
outputs = self(images)
diff --git a/src/mednet/libs/segmentation/scripts/train.py b/src/mednet/libs/segmentation/scripts/train.py
index 2632369c..67477db3 100644
--- a/src/mednet/libs/segmentation/scripts/train.py
+++ b/src/mednet/libs/segmentation/scripts/train.py
@@ -14,7 +14,7 @@ logger = setup("mednet", format="%(levelname)s: %(message)s")
@click.command(
- entry_point_group="mednet.libs.classification.config",
+ entry_point_group="mednet.libs.segmentation.config",
cls=ConfigCommand,
epilog="""Examples:
@@ -41,7 +41,6 @@ def train(
seed,
parallel,
monitoring_interval,
- balance_classes,
**_,
) -> None: # numpydoc ignore=PR01
"""Train an CNN to perform image classification.
@@ -89,7 +88,6 @@ def train(
seed,
parallel,
monitoring_interval,
- balance_classes,
)
run(
--
GitLab