From 3026dc35b00a5385c34af2a0b65236f4db535ffb Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Thu, 6 Jun 2024 16:44:56 +0200
Subject: [PATCH] [segmentation] Add jsrt database
---
pyproject.toml | 3 +
.../segmentation/config/data/jsrt/__init__.py | 0
.../config/data/jsrt/datamodule.py | 138 ++
.../config/data/jsrt/default.json | 1243 +++++++++++++++++
.../segmentation/config/data/jsrt/default.py | 16 +
.../models/histograms_lwnet_jsrt_default.json | 23 +
.../raw_data/histograms_jsrt_default.json | 23 +
.../libs/segmentation/tests/test_jsrt.py | 133 ++
8 files changed, 1579 insertions(+)
create mode 100644 src/mednet/libs/segmentation/config/data/jsrt/__init__.py
create mode 100644 src/mednet/libs/segmentation/config/data/jsrt/datamodule.py
create mode 100644 src/mednet/libs/segmentation/config/data/jsrt/default.json
create mode 100644 src/mednet/libs/segmentation/config/data/jsrt/default.py
create mode 100644 src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_jsrt_default.json
create mode 100644 src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_jsrt_default.json
create mode 100644 src/mednet/libs/segmentation/tests/test_jsrt.py
diff --git a/pyproject.toml b/pyproject.toml
index a3e40810..3e554e55 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -453,6 +453,9 @@ hrf = "mednet.libs.segmentation.config.data.hrf.default"
iostar-vessel = "mednet.libs.segmentation.config.data.iostar.vessel"
iostar-disc = "mednet.libs.segmentation.config.data.iostar.optic_disc"
+# jsrt - cxr
+jsrt = "mednet.libs.segmentation.config.data.jsrt.default"
+
# montgomery county - cxr
montgomery = "mednet.libs.segmentation.config.data.montgomery.default"
diff --git a/src/mednet/libs/segmentation/config/data/jsrt/__init__.py b/src/mednet/libs/segmentation/config/data/jsrt/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/mednet/libs/segmentation/config/data/jsrt/datamodule.py b/src/mednet/libs/segmentation/config/data/jsrt/datamodule.py
new file mode 100644
index 00000000..8f6aad49
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/jsrt/datamodule.py
@@ -0,0 +1,138 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""Japanese Society of Radiological Technology dataset for Lung Segmentation."""
+
+import os
+import pathlib
+
+import numpy as np
+import PIL.Image
+import skimage.exposure
+import torch
+from mednet.libs.common.data.datamodule import CachingDataModule
+from mednet.libs.common.data.split import make_split
+from mednet.libs.common.data.typing import Sample
+from mednet.libs.segmentation.data.typing import (
+ SegmentationRawDataLoader as _SegmentationRawDataLoader,
+)
+from torchvision import tv_tensors
+from torchvision.transforms.functional import to_tensor
+
+from ....utils.rc import load_rc
+
+CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
+"""Key to search for in the configuration file for the root directory of this
+database."""
+
+
+class SegmentationRawDataLoader(_SegmentationRawDataLoader):
+ """A specialized raw-data-loader for the drishtigs1jsrt dataset."""
+
+ datadir: pathlib.Path
+ """This variable contains the base directory where the database raw data is
+ stored."""
+
+ def __init__(self):
+ self.datadir = pathlib.Path(
+ load_rc().get(CONFIGURATION_KEY_DATADIR, os.path.realpath(os.curdir))
+ )
+
+ def load_pil_raw_12bit_jsrt(self, path: pathlib.Path) -> PIL.Image.Image:
+ """Load a raw 16-bit sample data.
+
+ This method was designed to handle the raw images from the JSRT_ dataset.
+ It reads the data file and applies a simple histogram equalization to the
+ 8-bit representation of the image to obtain something along the lines of
+ the PNG (unofficial) version distributed at `JSRT-Kaggle`_.
+
+ Parameters
+ ----------
+ path
+ The full path leading to the image to be loaded.
+
+ Returns
+ -------
+ A PIL image in RGB mode, with `width`x`width` pixels.
+ """
+
+ raw_image = np.fromfile(path, np.dtype(">u2")).reshape(2048, 2048)
+ raw_image[raw_image > 4095] = 4095
+ raw_image = 4095 - raw_image # invert colors
+ raw_image = (raw_image >> 4).astype(np.uint8) # 8-bit uint
+ raw_image = skimage.exposure.equalize_hist(raw_image)
+ return PIL.Image.fromarray((raw_image * 255).astype(np.uint8)).convert("RGB")
+
+ def sample(self, sample: tuple[str, str, str]) -> Sample:
+ """Load a single image sample from the disk.
+
+ Parameters
+ ----------
+ sample
+ A tuple containing the path suffix, within the dataset root folder,
+ where to find the image to be loaded, and an integer, representing the
+ sample label.
+
+ Returns
+ -------
+ The sample representation.
+ """
+
+ image = to_tensor(self.load_pil_raw_12bit_jsrt(self.datadir / sample[0]))
+
+ # Combine left and right lung masks into a single tensor
+ target = tv_tensors.Image(
+ to_tensor(
+ np.ma.mask_or(
+ np.asarray(
+ PIL.Image.open(self.datadir / sample[1]).convert(
+ mode="1", dither=None
+ )
+ ),
+ np.asarray(
+ PIL.Image.open(self.datadir / sample[2]).convert(
+ mode="1", dither=None
+ )
+ ),
+ )
+ ).float()
+ )
+
+ tensor = tv_tensors.Image(image)
+ target = tv_tensors.Image(target)
+ mask = tv_tensors.Mask(torch.ones_like(target))
+
+ return tensor, dict(target=target, mask=mask, name=sample[0]) # type: ignore[arg-type]
+
+
+class DataModule(CachingDataModule):
+ """Japanese Society of Radiological Technology dataset for Lung Segmentation.
+
+ The database includes 154 nodule and 93 non-nodule images. It contains a total
+ of 247 resolution of 2048 x 2048. One set of ground-truth lung annotations is
+ available.
+
+ * Reference: [JSRT-2000]_
+ * Original resolution (height x width): 2048 x 2048
+ * Configuration resolution: 1024 x 1024 (after rescaling)
+ * Split reference: [GAAL-2020]_
+ * Protocol ``default``:
+
+ * Training samples: 172 (including labels)
+ * Validation samples: 25 (including labels)
+ * Test samples: 50 (including labels)
+
+ Parameters
+ ----------
+ split_filename
+ Name of the .json file containing the split to load.
+ """
+
+ def __init__(self, split_filename: str):
+ assert __package__ is not None
+ super().__init__(
+ database_split=make_split(__package__, split_filename),
+ raw_data_loader=SegmentationRawDataLoader(),
+ database_name=__package__.rsplit(".", 1)[1],
+ split_name=pathlib.Path(split_filename).stem,
+ )
diff --git a/src/mednet/libs/segmentation/config/data/jsrt/default.json b/src/mednet/libs/segmentation/config/data/jsrt/default.json
new file mode 100644
index 00000000..e15ec844
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/jsrt/default.json
@@ -0,0 +1,1243 @@
+{
+ "train": [
+ [
+ "All247images/JPCLN049.IMG",
+ "scratch/fold1/masks/left lung/JPCLN049.gif",
+ "scratch/fold1/masks/right lung/JPCLN049.gif"
+ ],
+ [
+ "All247images/JPCNN064.IMG",
+ "scratch/fold2/masks/left lung/JPCNN064.gif",
+ "scratch/fold2/masks/right lung/JPCNN064.gif"
+ ],
+ [
+ "All247images/JPCLN102.IMG",
+ "scratch/fold2/masks/left lung/JPCLN102.gif",
+ "scratch/fold2/masks/right lung/JPCLN102.gif"
+ ],
+ [
+ "All247images/JPCLN039.IMG",
+ "scratch/fold1/masks/left lung/JPCLN039.gif",
+ "scratch/fold1/masks/right lung/JPCLN039.gif"
+ ],
+ [
+ "All247images/JPCLN087.IMG",
+ "scratch/fold1/masks/left lung/JPCLN087.gif",
+ "scratch/fold1/masks/right lung/JPCLN087.gif"
+ ],
+ [
+ "All247images/JPCLN104.IMG",
+ "scratch/fold2/masks/left lung/JPCLN104.gif",
+ "scratch/fold2/masks/right lung/JPCLN104.gif"
+ ],
+ [
+ "All247images/JPCLN079.IMG",
+ "scratch/fold1/masks/left lung/JPCLN079.gif",
+ "scratch/fold1/masks/right lung/JPCLN079.gif"
+ ],
+ [
+ "All247images/JPCNN046.IMG",
+ "scratch/fold2/masks/left lung/JPCNN046.gif",
+ "scratch/fold2/masks/right lung/JPCNN046.gif"
+ ],
+ [
+ "All247images/JPCLN081.IMG",
+ "scratch/fold1/masks/left lung/JPCLN081.gif",
+ "scratch/fold1/masks/right lung/JPCLN081.gif"
+ ],
+ [
+ "All247images/JPCLN096.IMG",
+ "scratch/fold2/masks/left lung/JPCLN096.gif",
+ "scratch/fold2/masks/right lung/JPCLN096.gif"
+ ],
+ [
+ "All247images/JPCNN022.IMG",
+ "scratch/fold2/masks/left lung/JPCNN022.gif",
+ "scratch/fold2/masks/right lung/JPCNN022.gif"
+ ],
+ [
+ "All247images/JPCLN065.IMG",
+ "scratch/fold1/masks/left lung/JPCLN065.gif",
+ "scratch/fold1/masks/right lung/JPCLN065.gif"
+ ],
+ [
+ "All247images/JPCLN137.IMG",
+ "scratch/fold1/masks/left lung/JPCLN137.gif",
+ "scratch/fold1/masks/right lung/JPCLN137.gif"
+ ],
+ [
+ "All247images/JPCLN139.IMG",
+ "scratch/fold1/masks/left lung/JPCLN139.gif",
+ "scratch/fold1/masks/right lung/JPCLN139.gif"
+ ],
+ [
+ "All247images/JPCLN029.IMG",
+ "scratch/fold1/masks/left lung/JPCLN029.gif",
+ "scratch/fold1/masks/right lung/JPCLN029.gif"
+ ],
+ [
+ "All247images/JPCNN083.IMG",
+ "scratch/fold1/masks/left lung/JPCNN083.gif",
+ "scratch/fold1/masks/right lung/JPCNN083.gif"
+ ],
+ [
+ "All247images/JPCLN038.IMG",
+ "scratch/fold2/masks/left lung/JPCLN038.gif",
+ "scratch/fold2/masks/right lung/JPCLN038.gif"
+ ],
+ [
+ "All247images/JPCLN088.IMG",
+ "scratch/fold2/masks/left lung/JPCLN088.gif",
+ "scratch/fold2/masks/right lung/JPCLN088.gif"
+ ],
+ [
+ "All247images/JPCNN005.IMG",
+ "scratch/fold1/masks/left lung/JPCNN005.gif",
+ "scratch/fold1/masks/right lung/JPCNN005.gif"
+ ],
+ [
+ "All247images/JPCLN055.IMG",
+ "scratch/fold1/masks/left lung/JPCLN055.gif",
+ "scratch/fold1/masks/right lung/JPCLN055.gif"
+ ],
+ [
+ "All247images/JPCNN056.IMG",
+ "scratch/fold2/masks/left lung/JPCNN056.gif",
+ "scratch/fold2/masks/right lung/JPCNN056.gif"
+ ],
+ [
+ "All247images/JPCLN001.IMG",
+ "scratch/fold1/masks/left lung/JPCLN001.gif",
+ "scratch/fold1/masks/right lung/JPCLN001.gif"
+ ],
+ [
+ "All247images/JPCNN063.IMG",
+ "scratch/fold1/masks/left lung/JPCNN063.gif",
+ "scratch/fold1/masks/right lung/JPCNN063.gif"
+ ],
+ [
+ "All247images/JPCLN072.IMG",
+ "scratch/fold2/masks/left lung/JPCLN072.gif",
+ "scratch/fold2/masks/right lung/JPCLN072.gif"
+ ],
+ [
+ "All247images/JPCNN039.IMG",
+ "scratch/fold1/masks/left lung/JPCNN039.gif",
+ "scratch/fold1/masks/right lung/JPCNN039.gif"
+ ],
+ [
+ "All247images/JPCNN004.IMG",
+ "scratch/fold2/masks/left lung/JPCNN004.gif",
+ "scratch/fold2/masks/right lung/JPCNN004.gif"
+ ],
+ [
+ "All247images/JPCNN038.IMG",
+ "scratch/fold2/masks/left lung/JPCNN038.gif",
+ "scratch/fold2/masks/right lung/JPCNN038.gif"
+ ],
+ [
+ "All247images/JPCLN012.IMG",
+ "scratch/fold2/masks/left lung/JPCLN012.gif",
+ "scratch/fold2/masks/right lung/JPCLN012.gif"
+ ],
+ [
+ "All247images/JPCLN076.IMG",
+ "scratch/fold2/masks/left lung/JPCLN076.gif",
+ "scratch/fold2/masks/right lung/JPCLN076.gif"
+ ],
+ [
+ "All247images/JPCNN014.IMG",
+ "scratch/fold2/masks/left lung/JPCNN014.gif",
+ "scratch/fold2/masks/right lung/JPCNN014.gif"
+ ],
+ [
+ "All247images/JPCLN078.IMG",
+ "scratch/fold2/masks/left lung/JPCLN078.gif",
+ "scratch/fold2/masks/right lung/JPCLN078.gif"
+ ],
+ [
+ "All247images/JPCLN101.IMG",
+ "scratch/fold1/masks/left lung/JPCLN101.gif",
+ "scratch/fold1/masks/right lung/JPCLN101.gif"
+ ],
+ [
+ "All247images/JPCLN126.IMG",
+ "scratch/fold2/masks/left lung/JPCLN126.gif",
+ "scratch/fold2/masks/right lung/JPCLN126.gif"
+ ],
+ [
+ "All247images/JPCNN086.IMG",
+ "scratch/fold2/masks/left lung/JPCNN086.gif",
+ "scratch/fold2/masks/right lung/JPCNN086.gif"
+ ],
+ [
+ "All247images/JPCLN082.IMG",
+ "scratch/fold2/masks/left lung/JPCLN082.gif",
+ "scratch/fold2/masks/right lung/JPCLN082.gif"
+ ],
+ [
+ "All247images/JPCNN001.IMG",
+ "scratch/fold1/masks/left lung/JPCNN001.gif",
+ "scratch/fold1/masks/right lung/JPCNN001.gif"
+ ],
+ [
+ "All247images/JPCLN099.IMG",
+ "scratch/fold1/masks/left lung/JPCLN099.gif",
+ "scratch/fold1/masks/right lung/JPCLN099.gif"
+ ],
+ [
+ "All247images/JPCLN154.IMG",
+ "scratch/fold2/masks/left lung/JPCLN154.gif",
+ "scratch/fold2/masks/right lung/JPCLN154.gif"
+ ],
+ [
+ "All247images/JPCLN010.IMG",
+ "scratch/fold2/masks/left lung/JPCLN010.gif",
+ "scratch/fold2/masks/right lung/JPCLN010.gif"
+ ],
+ [
+ "All247images/JPCLN148.IMG",
+ "scratch/fold2/masks/left lung/JPCLN148.gif",
+ "scratch/fold2/masks/right lung/JPCLN148.gif"
+ ],
+ [
+ "All247images/JPCNN027.IMG",
+ "scratch/fold1/masks/left lung/JPCNN027.gif",
+ "scratch/fold1/masks/right lung/JPCNN027.gif"
+ ],
+ [
+ "All247images/JPCLN129.IMG",
+ "scratch/fold1/masks/left lung/JPCLN129.gif",
+ "scratch/fold1/masks/right lung/JPCLN129.gif"
+ ],
+ [
+ "All247images/JPCNN080.IMG",
+ "scratch/fold2/masks/left lung/JPCNN080.gif",
+ "scratch/fold2/masks/right lung/JPCNN080.gif"
+ ],
+ [
+ "All247images/JPCLN094.IMG",
+ "scratch/fold2/masks/left lung/JPCLN094.gif",
+ "scratch/fold2/masks/right lung/JPCLN094.gif"
+ ],
+ [
+ "All247images/JPCLN125.IMG",
+ "scratch/fold1/masks/left lung/JPCLN125.gif",
+ "scratch/fold1/masks/right lung/JPCLN125.gif"
+ ],
+ [
+ "All247images/JPCLN149.IMG",
+ "scratch/fold1/masks/left lung/JPCLN149.gif",
+ "scratch/fold1/masks/right lung/JPCLN149.gif"
+ ],
+ [
+ "All247images/JPCNN034.IMG",
+ "scratch/fold2/masks/left lung/JPCNN034.gif",
+ "scratch/fold2/masks/right lung/JPCNN034.gif"
+ ],
+ [
+ "All247images/JPCNN028.IMG",
+ "scratch/fold2/masks/left lung/JPCNN028.gif",
+ "scratch/fold2/masks/right lung/JPCNN028.gif"
+ ],
+ [
+ "All247images/JPCNN067.IMG",
+ "scratch/fold1/masks/left lung/JPCNN067.gif",
+ "scratch/fold1/masks/right lung/JPCNN067.gif"
+ ],
+ [
+ "All247images/JPCNN009.IMG",
+ "scratch/fold1/masks/left lung/JPCNN009.gif",
+ "scratch/fold1/masks/right lung/JPCNN009.gif"
+ ],
+ [
+ "All247images/JPCLN020.IMG",
+ "scratch/fold2/masks/left lung/JPCLN020.gif",
+ "scratch/fold2/masks/right lung/JPCLN020.gif"
+ ],
+ [
+ "All247images/JPCNN058.IMG",
+ "scratch/fold2/masks/left lung/JPCNN058.gif",
+ "scratch/fold2/masks/right lung/JPCNN058.gif"
+ ],
+ [
+ "All247images/JPCNN041.IMG",
+ "scratch/fold1/masks/left lung/JPCNN041.gif",
+ "scratch/fold1/masks/right lung/JPCNN041.gif"
+ ],
+ [
+ "All247images/JPCLN095.IMG",
+ "scratch/fold1/masks/left lung/JPCLN095.gif",
+ "scratch/fold1/masks/right lung/JPCLN095.gif"
+ ],
+ [
+ "All247images/JPCNN084.IMG",
+ "scratch/fold2/masks/left lung/JPCNN084.gif",
+ "scratch/fold2/masks/right lung/JPCNN084.gif"
+ ],
+ [
+ "All247images/JPCLN014.IMG",
+ "scratch/fold2/masks/left lung/JPCLN014.gif",
+ "scratch/fold2/masks/right lung/JPCLN014.gif"
+ ],
+ [
+ "All247images/JPCNN015.IMG",
+ "scratch/fold1/masks/left lung/JPCNN015.gif",
+ "scratch/fold1/masks/right lung/JPCNN015.gif"
+ ],
+ [
+ "All247images/JPCNN081.IMG",
+ "scratch/fold1/masks/left lung/JPCNN081.gif",
+ "scratch/fold1/masks/right lung/JPCNN081.gif"
+ ],
+ [
+ "All247images/JPCLN052.IMG",
+ "scratch/fold2/masks/left lung/JPCLN052.gif",
+ "scratch/fold2/masks/right lung/JPCLN052.gif"
+ ],
+ [
+ "All247images/JPCLN113.IMG",
+ "scratch/fold1/masks/left lung/JPCLN113.gif",
+ "scratch/fold1/masks/right lung/JPCLN113.gif"
+ ],
+ [
+ "All247images/JPCLN121.IMG",
+ "scratch/fold1/masks/left lung/JPCLN121.gif",
+ "scratch/fold1/masks/right lung/JPCLN121.gif"
+ ],
+ [
+ "All247images/JPCLN141.IMG",
+ "scratch/fold1/masks/left lung/JPCLN141.gif",
+ "scratch/fold1/masks/right lung/JPCLN141.gif"
+ ],
+ [
+ "All247images/JPCLN085.IMG",
+ "scratch/fold1/masks/left lung/JPCLN085.gif",
+ "scratch/fold1/masks/right lung/JPCLN085.gif"
+ ],
+ [
+ "All247images/JPCLN035.IMG",
+ "scratch/fold1/masks/left lung/JPCLN035.gif",
+ "scratch/fold1/masks/right lung/JPCLN035.gif"
+ ],
+ [
+ "All247images/JPCLN070.IMG",
+ "scratch/fold2/masks/left lung/JPCLN070.gif",
+ "scratch/fold2/masks/right lung/JPCLN070.gif"
+ ],
+ [
+ "All247images/JPCLN005.IMG",
+ "scratch/fold1/masks/left lung/JPCLN005.gif",
+ "scratch/fold1/masks/right lung/JPCLN005.gif"
+ ],
+ [
+ "All247images/JPCLN145.IMG",
+ "scratch/fold1/masks/left lung/JPCLN145.gif",
+ "scratch/fold1/masks/right lung/JPCLN145.gif"
+ ],
+ [
+ "All247images/JPCNN047.IMG",
+ "scratch/fold1/masks/left lung/JPCNN047.gif",
+ "scratch/fold1/masks/right lung/JPCNN047.gif"
+ ],
+ [
+ "All247images/JPCLN017.IMG",
+ "scratch/fold1/masks/left lung/JPCLN017.gif",
+ "scratch/fold1/masks/right lung/JPCLN017.gif"
+ ],
+ [
+ "All247images/JPCNN011.IMG",
+ "scratch/fold1/masks/left lung/JPCNN011.gif",
+ "scratch/fold1/masks/right lung/JPCNN011.gif"
+ ],
+ [
+ "All247images/JPCLN152.IMG",
+ "scratch/fold2/masks/left lung/JPCLN152.gif",
+ "scratch/fold2/masks/right lung/JPCLN152.gif"
+ ],
+ [
+ "All247images/JPCLN004.IMG",
+ "scratch/fold2/masks/left lung/JPCLN004.gif",
+ "scratch/fold2/masks/right lung/JPCLN004.gif"
+ ],
+ [
+ "All247images/JPCNN093.IMG",
+ "scratch/fold1/masks/left lung/JPCNN093.gif",
+ "scratch/fold1/masks/right lung/JPCNN093.gif"
+ ],
+ [
+ "All247images/JPCLN131.IMG",
+ "scratch/fold1/masks/left lung/JPCLN131.gif",
+ "scratch/fold1/masks/right lung/JPCLN131.gif"
+ ],
+ [
+ "All247images/JPCNN049.IMG",
+ "scratch/fold1/masks/left lung/JPCNN049.gif",
+ "scratch/fold1/masks/right lung/JPCNN049.gif"
+ ],
+ [
+ "All247images/JPCNN045.IMG",
+ "scratch/fold1/masks/left lung/JPCNN045.gif",
+ "scratch/fold1/masks/right lung/JPCNN045.gif"
+ ],
+ [
+ "All247images/JPCNN052.IMG",
+ "scratch/fold2/masks/left lung/JPCNN052.gif",
+ "scratch/fold2/masks/right lung/JPCNN052.gif"
+ ],
+ [
+ "All247images/JPCLN098.IMG",
+ "scratch/fold2/masks/left lung/JPCLN098.gif",
+ "scratch/fold2/masks/right lung/JPCLN098.gif"
+ ],
+ [
+ "All247images/JPCNN035.IMG",
+ "scratch/fold1/masks/left lung/JPCNN035.gif",
+ "scratch/fold1/masks/right lung/JPCNN035.gif"
+ ],
+ [
+ "All247images/JPCLN115.IMG",
+ "scratch/fold1/masks/left lung/JPCLN115.gif",
+ "scratch/fold1/masks/right lung/JPCLN115.gif"
+ ],
+ [
+ "All247images/JPCLN047.IMG",
+ "scratch/fold1/masks/left lung/JPCLN047.gif",
+ "scratch/fold1/masks/right lung/JPCLN047.gif"
+ ],
+ [
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+ "scratch/fold2/masks/right lung/JPCNN026.gif"
+ ],
+ [
+ "All247images/JPCLN009.IMG",
+ "scratch/fold1/masks/left lung/JPCLN009.gif",
+ "scratch/fold1/masks/right lung/JPCLN009.gif"
+ ],
+ [
+ "All247images/JPCNN054.IMG",
+ "scratch/fold2/masks/left lung/JPCNN054.gif",
+ "scratch/fold2/masks/right lung/JPCNN054.gif"
+ ],
+ [
+ "All247images/JPCLN061.IMG",
+ "scratch/fold1/masks/left lung/JPCLN061.gif",
+ "scratch/fold1/masks/right lung/JPCLN061.gif"
+ ],
+ [
+ "All247images/JPCLN050.IMG",
+ "scratch/fold2/masks/left lung/JPCLN050.gif",
+ "scratch/fold2/masks/right lung/JPCLN050.gif"
+ ],
+ [
+ "All247images/JPCLN051.IMG",
+ "scratch/fold1/masks/left lung/JPCLN051.gif",
+ "scratch/fold1/masks/right lung/JPCLN051.gif"
+ ],
+ [
+ "All247images/JPCLN084.IMG",
+ "scratch/fold2/masks/left lung/JPCLN084.gif",
+ "scratch/fold2/masks/right lung/JPCLN084.gif"
+ ],
+ [
+ "All247images/JPCLN028.IMG",
+ "scratch/fold2/masks/left lung/JPCLN028.gif",
+ "scratch/fold2/masks/right lung/JPCLN028.gif"
+ ],
+ [
+ "All247images/JPCLN057.IMG",
+ "scratch/fold1/masks/left lung/JPCLN057.gif",
+ "scratch/fold1/masks/right lung/JPCLN057.gif"
+ ],
+ [
+ "All247images/JPCLN142.IMG",
+ "scratch/fold2/masks/left lung/JPCLN142.gif",
+ "scratch/fold2/masks/right lung/JPCLN142.gif"
+ ],
+ [
+ "All247images/JPCLN122.IMG",
+ "scratch/fold2/masks/left lung/JPCLN122.gif",
+ "scratch/fold2/masks/right lung/JPCLN122.gif"
+ ],
+ [
+ "All247images/JPCNN029.IMG",
+ "scratch/fold1/masks/left lung/JPCNN029.gif",
+ "scratch/fold1/masks/right lung/JPCNN029.gif"
+ ],
+ [
+ "All247images/JPCLN045.IMG",
+ "scratch/fold1/masks/left lung/JPCLN045.gif",
+ "scratch/fold1/masks/right lung/JPCLN045.gif"
+ ],
+ [
+ "All247images/JPCLN003.IMG",
+ "scratch/fold1/masks/left lung/JPCLN003.gif",
+ "scratch/fold1/masks/right lung/JPCLN003.gif"
+ ],
+ [
+ "All247images/JPCNN068.IMG",
+ "scratch/fold2/masks/left lung/JPCNN068.gif",
+ "scratch/fold2/masks/right lung/JPCNN068.gif"
+ ],
+ [
+ "All247images/JPCLN134.IMG",
+ "scratch/fold2/masks/left lung/JPCLN134.gif",
+ "scratch/fold2/masks/right lung/JPCLN134.gif"
+ ],
+ [
+ "All247images/JPCLN062.IMG",
+ "scratch/fold2/masks/left lung/JPCLN062.gif",
+ "scratch/fold2/masks/right lung/JPCLN062.gif"
+ ],
+ [
+ "All247images/JPCLN033.IMG",
+ "scratch/fold1/masks/left lung/JPCLN033.gif",
+ "scratch/fold1/masks/right lung/JPCLN033.gif"
+ ],
+ [
+ "All247images/JPCNN024.IMG",
+ "scratch/fold2/masks/left lung/JPCNN024.gif",
+ "scratch/fold2/masks/right lung/JPCNN024.gif"
+ ],
+ [
+ "All247images/JPCNN077.IMG",
+ "scratch/fold1/masks/left lung/JPCNN077.gif",
+ "scratch/fold1/masks/right lung/JPCNN077.gif"
+ ],
+ [
+ "All247images/JPCLN031.IMG",
+ "scratch/fold1/masks/left lung/JPCLN031.gif",
+ "scratch/fold1/masks/right lung/JPCLN031.gif"
+ ],
+ [
+ "All247images/JPCNN032.IMG",
+ "scratch/fold2/masks/left lung/JPCNN032.gif",
+ "scratch/fold2/masks/right lung/JPCNN032.gif"
+ ],
+ [
+ "All247images/JPCNN076.IMG",
+ "scratch/fold2/masks/left lung/JPCNN076.gif",
+ "scratch/fold2/masks/right lung/JPCNN076.gif"
+ ],
+ [
+ "All247images/JPCNN069.IMG",
+ "scratch/fold1/masks/left lung/JPCNN069.gif",
+ "scratch/fold1/masks/right lung/JPCNN069.gif"
+ ],
+ [
+ "All247images/JPCNN013.IMG",
+ "scratch/fold1/masks/left lung/JPCNN013.gif",
+ "scratch/fold1/masks/right lung/JPCNN013.gif"
+ ],
+ [
+ "All247images/JPCNN066.IMG",
+ "scratch/fold2/masks/left lung/JPCNN066.gif",
+ "scratch/fold2/masks/right lung/JPCNN066.gif"
+ ],
+ [
+ "All247images/JPCLN007.IMG",
+ "scratch/fold1/masks/left lung/JPCLN007.gif",
+ "scratch/fold1/masks/right lung/JPCLN007.gif"
+ ],
+ [
+ "All247images/JPCLN064.IMG",
+ "scratch/fold2/masks/left lung/JPCLN064.gif",
+ "scratch/fold2/masks/right lung/JPCLN064.gif"
+ ],
+ [
+ "All247images/JPCLN132.IMG",
+ "scratch/fold2/masks/left lung/JPCLN132.gif",
+ "scratch/fold2/masks/right lung/JPCLN132.gif"
+ ],
+ [
+ "All247images/JPCNN073.IMG",
+ "scratch/fold1/masks/left lung/JPCNN073.gif",
+ "scratch/fold1/masks/right lung/JPCNN073.gif"
+ ],
+ [
+ "All247images/JPCLN011.IMG",
+ "scratch/fold1/masks/left lung/JPCLN011.gif",
+ "scratch/fold1/masks/right lung/JPCLN011.gif"
+ ],
+ [
+ "All247images/JPCNN031.IMG",
+ "scratch/fold1/masks/left lung/JPCNN031.gif",
+ "scratch/fold1/masks/right lung/JPCNN031.gif"
+ ],
+ [
+ "All247images/JPCLN042.IMG",
+ "scratch/fold2/masks/left lung/JPCLN042.gif",
+ "scratch/fold2/masks/right lung/JPCLN042.gif"
+ ],
+ [
+ "All247images/JPCLN018.IMG",
+ "scratch/fold2/masks/left lung/JPCLN018.gif",
+ "scratch/fold2/masks/right lung/JPCLN018.gif"
+ ],
+ [
+ "All247images/JPCLN130.IMG",
+ "scratch/fold2/masks/left lung/JPCLN130.gif",
+ "scratch/fold2/masks/right lung/JPCLN130.gif"
+ ],
+ [
+ "All247images/JPCLN008.IMG",
+ "scratch/fold2/masks/left lung/JPCLN008.gif",
+ "scratch/fold2/masks/right lung/JPCLN008.gif"
+ ],
+ [
+ "All247images/JPCNN019.IMG",
+ "scratch/fold1/masks/left lung/JPCNN019.gif",
+ "scratch/fold1/masks/right lung/JPCNN019.gif"
+ ],
+ [
+ "All247images/JPCNN059.IMG",
+ "scratch/fold1/masks/left lung/JPCNN059.gif",
+ "scratch/fold1/masks/right lung/JPCNN059.gif"
+ ],
+ [
+ "All247images/JPCLN040.IMG",
+ "scratch/fold2/masks/left lung/JPCLN040.gif",
+ "scratch/fold2/masks/right lung/JPCLN040.gif"
+ ],
+ [
+ "All247images/JPCLN069.IMG",
+ "scratch/fold1/masks/left lung/JPCLN069.gif",
+ "scratch/fold1/masks/right lung/JPCLN069.gif"
+ ],
+ [
+ "All247images/JPCLN032.IMG",
+ "scratch/fold2/masks/left lung/JPCLN032.gif",
+ "scratch/fold2/masks/right lung/JPCLN032.gif"
+ ],
+ [
+ "All247images/JPCLN023.IMG",
+ "scratch/fold1/masks/left lung/JPCLN023.gif",
+ "scratch/fold1/masks/right lung/JPCLN023.gif"
+ ],
+ [
+ "All247images/JPCNN020.IMG",
+ "scratch/fold2/masks/left lung/JPCNN020.gif",
+ "scratch/fold2/masks/right lung/JPCNN020.gif"
+ ],
+ [
+ "All247images/JPCNN087.IMG",
+ "scratch/fold1/masks/left lung/JPCNN087.gif",
+ "scratch/fold1/masks/right lung/JPCNN087.gif"
+ ],
+ [
+ "All247images/JPCLN058.IMG",
+ "scratch/fold2/masks/left lung/JPCLN058.gif",
+ "scratch/fold2/masks/right lung/JPCLN058.gif"
+ ],
+ [
+ "All247images/JPCLN151.IMG",
+ "scratch/fold1/masks/left lung/JPCLN151.gif",
+ "scratch/fold1/masks/right lung/JPCLN151.gif"
+ ],
+ [
+ "All247images/JPCLN135.IMG",
+ "scratch/fold1/masks/left lung/JPCLN135.gif",
+ "scratch/fold1/masks/right lung/JPCLN135.gif"
+ ],
+ [
+ "All247images/JPCLN144.IMG",
+ "scratch/fold2/masks/left lung/JPCLN144.gif",
+ "scratch/fold2/masks/right lung/JPCLN144.gif"
+ ],
+ [
+ "All247images/JPCNN088.IMG",
+ "scratch/fold2/masks/left lung/JPCNN088.gif",
+ "scratch/fold2/masks/right lung/JPCNN088.gif"
+ ],
+ [
+ "All247images/JPCLN112.IMG",
+ "scratch/fold2/masks/left lung/JPCLN112.gif",
+ "scratch/fold2/masks/right lung/JPCLN112.gif"
+ ]
+ ]
+}
diff --git a/src/mednet/libs/segmentation/config/data/jsrt/default.py b/src/mednet/libs/segmentation/config/data/jsrt/default.py
new file mode 100644
index 00000000..b4a552fa
--- /dev/null
+++ b/src/mednet/libs/segmentation/config/data/jsrt/default.py
@@ -0,0 +1,16 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""Japanese Society of Radiological Technology dataset for Lung Segmentation
+(default protocol).
+
+* Split reference: [GAAL-2020]_
+* Configuration resolution: 256 x 256
+* See :py:mod:`deepdraw.data.jsrt` for dataset details
+"""
+
+from mednet.libs.segmentation.config.data.jsrt.datamodule import (
+ DataModule,
+)
+
+datamodule = DataModule("default.json")
diff --git a/src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_jsrt_default.json b/src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_jsrt_default.json
new file mode 100644
index 00000000..4fd46d93
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/data/histograms/models/histograms_lwnet_jsrt_default.json
@@ -0,0 +1,23 @@
+{
+ "train": [
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+ ],
+ "test": [
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+ ]
+}
diff --git a/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_jsrt_default.json b/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_jsrt_default.json
new file mode 100644
index 00000000..bdd227b7
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/data/histograms/raw_data/histograms_jsrt_default.json
@@ -0,0 +1,23 @@
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+ ["All247images/JPCLN064.IMG", [0, 0, 47806, 17496, 14303, 18857, 3879, 18666, 0, 33721, 25750, 14257, 11418, 23286, 8388, 22898, 18444, 15990, 15993, 16822, 16570, 15902, 16806, 15168, 16505, 10649, 12257, 13898, 15882, 16174, 16656, 16869, 17028, 18001, 19809, 21392, 0, 23883, 26040, 0, 28392, 0, 29723, 0, 30600, 0, 30651, 30950, 0, 30777, 0, 30955, 0, 32163, 0, 33080, 0, 33909, 0, 33833, 0, 34281, 0, 33139, 0, 32845, 0, 30973, 0, 29879, 0, 28697, 27554, 0, 26085, 0, 25867, 24569, 0, 24701, 24049, 0, 24049, 24086, 23475, 0, 23017, 22988, 0, 22219, 21996, 22334, 0, 22652, 22625, 22946, 0, 22501, 22236, 21386, 0, 21147, 21640, 21735, 0, 21994, 22986, 0, 23596, 24125, 24148, 0, 24417, 24086, 0, 23769, 23641, 0, 23864, 23793, 0, 23144, 23056, 23011, 0, 23043, 23205, 0, 23408, 23729, 0, 24135, 24905, 0, 24425, 24721, 0, 24935, 25015, 0, 25645, 26577, 0, 26850, 0, 27844, 28502, 0, 29502, 0, 30887, 0, 33286, 0, 36540, 0, 0, 39636, 0, 41679, 0, 0, 43822, 0, 0, 45971, 0, 0, 49490, 0, 0, 55177, 0, 0, 0, 62976, 0, 0, 0, 0, 77959, 0, 0, 0, 0, 85549, 0, 0, 0, 0, 78983, 0, 0, 63840, 0, 0, 0, 58082, 0, 0, 55606, 0, 0, 0, 56427, 0, 0, 55168, 0, 0, 0, 56904, 0, 0, 51302, 0, 0, 49150, 0, 43518, 0, 0, 40751, 0, 43861, 0, 0, 46997, 0, 0, 0, 52569, 0, 0, 59787, 0, 0, 0, 65352, 0, 0, 0, 68198, 0, 0, 0, 0, 0, 89568, 0, 0, 58663, 4353, 0, 0, 48015, 0, 0, 47806, 17496, 14303, 18857, 3879, 18666, 0, 33721, 25750, 14257, 11418, 23286, 8388, 22898, 18444, 15990, 15993, 16822, 16570, 15902, 16806, 15168, 16505, 10649, 12257, 13898, 15882, 16174, 16656, 16869, 17028, 18001, 19809, 21392, 0, 23883, 26040, 0, 28392, 0, 29723, 0, 30600, 0, 30651, 30950, 0, 30777, 0, 30955, 0, 32163, 0, 33080, 0, 33909, 0, 33833, 0, 34281, 0, 33139, 0, 32845, 0, 30973, 0, 29879, 0, 28697, 27554, 0, 26085, 0, 25867, 24569, 0, 24701, 24049, 0, 24049, 24086, 23475, 0, 23017, 22988, 0, 22219, 21996, 22334, 0, 22652, 22625, 22946, 0, 22501, 22236, 21386, 0, 21147, 21640, 21735, 0, 21994, 22986, 0, 23596, 24125, 24148, 0, 24417, 24086, 0, 23769, 23641, 0, 23864, 23793, 0, 23144, 23056, 23011, 0, 23043, 23205, 0, 23408, 23729, 0, 24135, 24905, 0, 24425, 24721, 0, 24935, 25015, 0, 25645, 26577, 0, 26850, 0, 27844, 28502, 0, 29502, 0, 30887, 0, 33286, 0, 36540, 0, 0, 39636, 0, 41679, 0, 0, 43822, 0, 0, 45971, 0, 0, 49490, 0, 0, 55177, 0, 0, 0, 62976, 0, 0, 0, 0, 77959, 0, 0, 0, 0, 85549, 0, 0, 0, 0, 78983, 0, 0, 63840, 0, 0, 0, 58082, 0, 0, 55606, 0, 0, 0, 56427, 0, 0, 55168, 0, 0, 0, 56904, 0, 0, 51302, 0, 0, 49150, 0, 43518, 0, 0, 40751, 0, 43861, 0, 0, 46997, 0, 0, 0, 52569, 0, 0, 59787, 0, 0, 0, 65352, 0, 0, 0, 68198, 0, 0, 0, 0, 0, 89568, 0, 0, 58663, 4353, 0, 0, 48015, 0, 0, 47806, 17496, 14303, 18857, 3879, 18666, 0, 33721, 25750, 14257, 11418, 23286, 8388, 22898, 18444, 15990, 15993, 16822, 16570, 15902, 16806, 15168, 16505, 10649, 12257, 13898, 15882, 16174, 16656, 16869, 17028, 18001, 19809, 21392, 0, 23883, 26040, 0, 28392, 0, 29723, 0, 30600, 0, 30651, 30950, 0, 30777, 0, 30955, 0, 32163, 0, 33080, 0, 33909, 0, 33833, 0, 34281, 0, 33139, 0, 32845, 0, 30973, 0, 29879, 0, 28697, 27554, 0, 26085, 0, 25867, 24569, 0, 24701, 24049, 0, 24049, 24086, 23475, 0, 23017, 22988, 0, 22219, 21996, 22334, 0, 22652, 22625, 22946, 0, 22501, 22236, 21386, 0, 21147, 21640, 21735, 0, 21994, 22986, 0, 23596, 24125, 24148, 0, 24417, 24086, 0, 23769, 23641, 0, 23864, 23793, 0, 23144, 23056, 23011, 0, 23043, 23205, 0, 23408, 23729, 0, 24135, 24905, 0, 24425, 24721, 0, 24935, 25015, 0, 25645, 26577, 0, 26850, 0, 27844, 28502, 0, 29502, 0, 30887, 0, 33286, 0, 36540, 0, 0, 39636, 0, 41679, 0, 0, 43822, 0, 0, 45971, 0, 0, 49490, 0, 0, 55177, 0, 0, 0, 62976, 0, 0, 0, 0, 77959, 0, 0, 0, 0, 85549, 0, 0, 0, 0, 78983, 0, 0, 63840, 0, 0, 0, 58082, 0, 0, 55606, 0, 0, 0, 56427, 0, 0, 55168, 0, 0, 0, 56904, 0, 0, 51302, 0, 0, 49150, 0, 43518, 0, 0, 40751, 0, 43861, 0, 0, 46997, 0, 0, 0, 52569, 0, 0, 59787, 0, 0, 0, 65352, 0, 0, 0, 68198, 0, 0, 0, 0, 0, 89568, 0, 0, 58663, 4353, 0, 0, 48015]]
+ ]
+}
diff --git a/src/mednet/libs/segmentation/tests/test_jsrt.py b/src/mednet/libs/segmentation/tests/test_jsrt.py
new file mode 100644
index 00000000..c096a130
--- /dev/null
+++ b/src/mednet/libs/segmentation/tests/test_jsrt.py
@@ -0,0 +1,133 @@
+# SPDX-FileCopyrightText: Copyright © 2024 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""Tests for jsrt dataset."""
+
+import importlib
+
+import pytest
+from click.testing import CliRunner
+
+
+def id_function(val):
+ if isinstance(val, dict):
+ return str(val)
+ return repr(val)
+
+
+@pytest.mark.parametrize(
+ "split,lengths",
+ [
+ ("default", dict(train=172, validation=25, test=50)),
+ ],
+ ids=id_function, # just changes how pytest prints it
+)
+def test_protocol_consistency(
+ database_checkers,
+ split: str,
+ lengths: dict[str, int],
+):
+ from mednet.libs.common.data.split import make_split
+
+ database_checkers.check_split(
+ make_split("mednet.libs.segmentation.config.data.jsrt", f"{split}.json"),
+ lengths=lengths,
+ )
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.jsrt")
+def test_database_check():
+ from mednet.libs.segmentation.scripts.database import check
+
+ runner = CliRunner()
+ result = runner.invoke(check, ["jsrt"])
+ assert (
+ result.exit_code == 0
+ ), f"Exit code {result.exit_code} != 0 -- Output:\n{result.output}"
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.jsrt")
+@pytest.mark.parametrize(
+ "dataset",
+ [
+ "train",
+ "validation",
+ "test",
+ ],
+)
+@pytest.mark.parametrize(
+ "name",
+ [
+ "default",
+ ],
+)
+def test_loading(database_checkers, name: str, dataset: str):
+ datamodule = importlib.import_module(
+ f".{name}",
+ "mednet.libs.segmentation.config.data.jsrt",
+ ).datamodule
+
+ datamodule.model_transforms = [] # should be done before setup()
+ datamodule.setup("predict") # sets up all datasets
+
+ loader = datamodule.predict_dataloader()[dataset]
+
+ limit = 3 # limit load checking
+ for batch in loader:
+ if limit == 0:
+ break
+ database_checkers.check_loaded_batch(
+ batch,
+ batch_size=1,
+ color_planes=3,
+ expected_num_targets=1,
+ )
+ limit -= 1
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.jsrt")
+def test_raw_transforms_image_quality(database_checkers, datadir):
+ reference_histogram_file = str(
+ datadir / "histograms/raw_data/histograms_jsrt_default.json",
+ )
+
+ datamodule = importlib.import_module(
+ ".default",
+ "mednet.libs.segmentation.config.data.jsrt",
+ ).datamodule
+
+ datamodule.model_transforms = []
+ datamodule.setup("predict")
+
+ database_checkers.check_image_quality(datamodule, reference_histogram_file)
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.jsrt")
+@pytest.mark.parametrize(
+ "model_name",
+ ["lwnet"],
+)
+def test_model_transforms_image_quality(database_checkers, datadir, model_name):
+ reference_histogram_file = str(
+ datadir / f"histograms/models/histograms_{model_name}_jsrt_default.json",
+ )
+
+ datamodule = importlib.import_module(
+ ".default",
+ "mednet.libs.segmentation.config.data.jsrt",
+ ).datamodule
+
+ model = importlib.import_module(
+ f".{model_name}",
+ "mednet.libs.segmentation.config.models",
+ ).model
+
+ datamodule.model_transforms = model.model_transforms
+ datamodule.setup("predict")
+
+ database_checkers.check_image_quality(
+ datamodule,
+ reference_histogram_file,
+ compare_type="statistical",
+ pearson_coeff_threshold=0.005,
+ )
--
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