From 229dd23c7d68c762d0f7f145986f07065c9fea48 Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Thu, 23 May 2024 13:27:19 +0200
Subject: [PATCH] [train-analysis] Fix input parameter issue
---
.../libs/classification/scripts/experiment.py | 2 +-
.../libs/common/scripts/train_analysis.py | 27 ++++++++-----------
src/mednet/libs/segmentation/models/typing.py | 7 ++---
3 files changed, 14 insertions(+), 22 deletions(-)
diff --git a/src/mednet/libs/classification/scripts/experiment.py b/src/mednet/libs/classification/scripts/experiment.py
index 6f11690a..5fdf8c6c 100644
--- a/src/mednet/libs/classification/scripts/experiment.py
+++ b/src/mednet/libs/classification/scripts/experiment.py
@@ -101,7 +101,7 @@ def experiment(
ctx.invoke(
train_analysis,
logdir=train_output_folder / "logs",
- output=output_folder / "trainlog.pdf",
+ output_folder=output_folder / "trainlog.pdf",
)
logger.info("Ended train analysis")
diff --git a/src/mednet/libs/common/scripts/train_analysis.py b/src/mednet/libs/common/scripts/train_analysis.py
index c3b1155c..f5295b1b 100644
--- a/src/mednet/libs/common/scripts/train_analysis.py
+++ b/src/mednet/libs/common/scripts/train_analysis.py
@@ -9,8 +9,6 @@ import click
from clapper.click import ResourceOption, verbosity_option
from clapper.logging import setup
-from .click import ConfigCommand
-
# avoids X11/graphical desktop requirement when creating plots
__import__("matplotlib").use("agg")
@@ -186,7 +184,6 @@ def _create_figures(
@click.command(
- cls=ConfigCommand,
epilog="""Examples:
\b
@@ -194,7 +191,7 @@ def _create_figures(
.. code:: sh
- mednet train-analysis -vv --log-dir=results/logs --output=trainlog.pdf
+ mednet train-analysis -vv results/logs
""",
)
@click.option(
@@ -203,19 +200,15 @@ def _create_figures(
help="Path to the directory containing the Tensorboard training logs",
required=True,
type=click.Path(dir_okay=True, exists=True, path_type=pathlib.Path),
- default="results/logs",
- cls=ResourceOption,
)
@click.option(
- "--output",
+ "--output-folder",
"-o",
- help="""Path to a PDF file in which to store results. (leading
- directories are created if they do not exist).""",
+ help="Directory in which to store results (created if does not exist)",
required=True,
- cls=ResourceOption,
type=click.Path(
- file_okay=True,
- dir_okay=False,
+ file_okay=False,
+ dir_okay=True,
writable=True,
path_type=pathlib.Path,
),
@@ -224,19 +217,21 @@ def _create_figures(
@verbosity_option(logger=logger, expose_value=False)
def train_analysis(
logdir: pathlib.Path,
- output: pathlib.Path,
- **_,
+ output_folder: pathlib.Path,
) -> None: # numpydoc ignore=PR01
"""Create a plot for each metric in the training logs and saves them in a .pdf file."""
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
from mednet.libs.common.utils.tensorboard import scalars_to_dict
+ train_log_filename = "trainlog.pdf"
+ train_log_file = pathlib.Path(output_folder) / train_log_filename
+
data = scalars_to_dict(logdir)
- output.parent.mkdir(parents=True, exist_ok=True)
+ train_log_file.parent.mkdir(parents=True, exist_ok=True)
- with PdfPages(output) as pdf:
+ with PdfPages(train_log_file) as pdf:
for figure in _create_figures(data):
pdf.savefig(figure)
plt.close(figure)
diff --git a/src/mednet/libs/segmentation/models/typing.py b/src/mednet/libs/segmentation/models/typing.py
index d452c519..5a24afb6 100644
--- a/src/mednet/libs/segmentation/models/typing.py
+++ b/src/mednet/libs/segmentation/models/typing.py
@@ -3,14 +3,11 @@
# SPDX-License-Identifier: GPL-3.0-or-later
"""Defines most common types used in code."""
+import pathlib
import typing
-import torch
-
Checkpoint: typing.TypeAlias = typing.MutableMapping[str, typing.Any]
"""Definition of a lightning checkpoint."""
-SegmentationPrediction: typing.TypeAlias = tuple[
- str, torch.Tensor, torch.Tensor, torch.Tensor
-]
+SegmentationPrediction: typing.TypeAlias = tuple[pathlib.Path, pathlib.Path]
"""The sample name, the target, and the predicted value."""
--
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