bids-mosaic 0.0.1__tar.gz

bids_mosaic-0.0.1/LICENSE.txt

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+MIT License
+
+Copyright (c) 2025 - present Joseph Wexler
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

bids_mosaic-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: bids-mosaic
+Version: 0.0.1
+Summary: A BIDS tool for creating PDFs containing slices of nifti images
+Author-email: Joseph Wexler <jbwexler@stanford.edu>
+License-Expression: MIT
+Project-URL: Source, https://github.com/jbwexler/bids-mosaic
+Classifier: Development Status :: 4 - Beta
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: pybids>=0.16.0
+Requires-Dist: nilearn>=0.10.0
+Requires-Dist: nibabel>=5.0.0
+Requires-Dist: reportlab>=3.6.12
+Requires-Dist: pillow>=9.3.0
+Requires-Dist: matplotlib>=3.7.0
+Dynamic: license-file
+
+## BIDS-Mosaic
+A BIDS tool for creating PDFs containing slices of nifti images
+
+## Installation
+```
+pip install bidsmosaic
+```
+
+## Usage
+```
+bids-mosiac <bids_dataset_directory>
+```
+
+For more options:
+```
+bids-mosaic --help
+```
+
+## Example
+![alt text](visuals/example.png)
+
+## License
+BIDS-Mosaic is licensed under [MIT license](LICENSE.txt).

bids_mosaic-0.0.1/README.md

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+## BIDS-Mosaic
+A BIDS tool for creating PDFs containing slices of nifti images
+
+## Installation
+```
+pip install bidsmosaic
+```
+
+## Usage
+```
+bids-mosiac <bids_dataset_directory>
+```
+
+For more options:
+```
+bids-mosaic --help
+```
+
+## Example
+![alt text](visuals/example.png)
+
+## License
+BIDS-Mosaic is licensed under [MIT license](LICENSE.txt).

bids_mosaic-0.0.1/bids_mosaic.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: bids-mosaic
+Version: 0.0.1
+Summary: A BIDS tool for creating PDFs containing slices of nifti images
+Author-email: Joseph Wexler <jbwexler@stanford.edu>
+License-Expression: MIT
+Project-URL: Source, https://github.com/jbwexler/bids-mosaic
+Classifier: Development Status :: 4 - Beta
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: pybids>=0.16.0
+Requires-Dist: nilearn>=0.10.0
+Requires-Dist: nibabel>=5.0.0
+Requires-Dist: reportlab>=3.6.12
+Requires-Dist: pillow>=9.3.0
+Requires-Dist: matplotlib>=3.7.0
+Dynamic: license-file
+
+## BIDS-Mosaic
+A BIDS tool for creating PDFs containing slices of nifti images
+
+## Installation
+```
+pip install bidsmosaic
+```
+
+## Usage
+```
+bids-mosiac <bids_dataset_directory>
+```
+
+For more options:
+```
+bids-mosaic --help
+```
+
+## Example
+![alt text](visuals/example.png)
+
+## License
+BIDS-Mosaic is licensed under [MIT license](LICENSE.txt).

bids_mosaic-0.0.1/bids_mosaic.egg-info/SOURCES.txt

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+LICENSE.txt
+README.md
+pyproject.toml
+bids_mosaic.egg-info/PKG-INFO
+bids_mosaic.egg-info/SOURCES.txt
+bids_mosaic.egg-info/dependency_links.txt
+bids_mosaic.egg-info/entry_points.txt
+bids_mosaic.egg-info/requires.txt
+bids_mosaic.egg-info/top_level.txt
+bidsmosaic/__init__.py
+bidsmosaic/mosaic.py

bids_mosaic-0.0.1/bids_mosaic.egg-info/dependency_links.txt

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+

bids_mosaic-0.0.1/bids_mosaic.egg-info/entry_points.txt

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+[console_scripts]
+bids-mosaic = bidsmosaic.mosaic:main

bids_mosaic-0.0.1/bids_mosaic.egg-info/requires.txt

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+numpy>=1.24.0
+pybids>=0.16.0
+nilearn>=0.10.0
+nibabel>=5.0.0
+reportlab>=3.6.12
+pillow>=9.3.0
+matplotlib>=3.7.0

bids_mosaic-0.0.1/bids_mosaic.egg-info/top_level.txt

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+bidsmosaic

bids_mosaic-0.0.1/bidsmosaic/mosaic.py

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+import numpy as np
+import argparse
+import os.path
+import glob
+import tempfile
+import json
+import logging
+import PIL.Image
+from bids import BIDSLayout
+from nilearn.plotting import plot_img
+import matplotlib.pyplot as plt
+import nibabel as nb
+from reportlab.platypus import (
+    Paragraph,
+    Image,
+    Table,
+    SimpleDocTemplate,
+    PageBreak,
+    TableStyle,
+    Spacer,
+)
+from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
+from reportlab.lib import colors
+
+
+logger = logging.getLogger(__name__)
+
+
+def enhance_brightness(
+    img: PIL.Image, target_brightness=100, threshold=10
+) -> PIL.Image:
+    """Attempts to change the brightness of an image to the target brightness."""
+    arr = np.array(img, dtype="float32")
+    mask = arr > threshold
+    rms = np.sqrt(np.mean(np.square(arr[mask])))
+    brightness_factor = target_brightness / rms
+    arr[mask] *= brightness_factor
+    return PIL.Image.fromarray(arr).convert("L")
+
+
+def create_slice_img(
+    img_path: str,
+    out_dir: str,
+    ds_path: str,
+    display_mode="x",
+    cut_coords=np.array([0]),
+    colorbar=False,
+    ds_root=None,
+    downsample=None,
+) -> None:
+    """Creates a png of a slice(s) of a nifti. Defaults to a single midline
+    sagittal slice."""
+
+    logger.debug(f"Creating png from {img_path}")
+    try:
+        img = nb.load(img_path)
+    except FileNotFoundError:
+        logger.warning("%s was not found." % img_path)
+        return
+
+    if ds_root:
+        relpath = os.path.relpath(img_path, ds_path)
+        out_file = relpath.replace("/", ":") + ".png"
+    else:
+        out_file = os.path.basename(img_path) + ".png"
+
+    out_path = os.path.join(out_dir, out_file)
+
+    plot_img(
+        img,
+        display_mode=display_mode,
+        cut_coords=cut_coords,
+        colorbar=colorbar,
+        annotate=False,
+    )
+    plt.savefig(out_path, transparent=True)
+    plt.close()
+
+    # Remove transparent margins
+    png = PIL.Image.open(out_path)
+    new_png = png.crop(png.getbbox()).convert("L")
+
+    if downsample:
+        height, width = new_png.size
+        new_size = (round(height / downsample), round(width / downsample))
+        new_png = new_png.resize(new_size)
+
+    new_png = enhance_brightness(new_png)
+
+    new_png.save(out_path)
+
+
+def create_sized_img(img_path: str, new_height: int) -> Image:
+    """Creates a reportlab Image from a .png. Resizes using new_height
+    and calculating new_width to maintain aspect ratio."""
+    img = PIL.Image.open(img_path)
+    width, height = img.size
+    new_width = (new_height / height) * width
+    return Image(img_path, height=new_height, width=new_width)
+
+
+def create_filename_caption(img_path: str) -> Paragraph:
+    """Creates a reportlab Paragraph containing the filename of the image."""
+    caption_text = os.path.basename(img_path)
+    caption_text = caption_text.replace(":", "/")
+    caption_text = os.path.relpath(caption_text)
+    caption_text = caption_text.removesuffix(".png")
+    return caption_text
+
+
+def create_mosaic_table(img_dir_path: str, page_width: int, styles) -> Table:
+    """Creates reportlab Table of slice images with image-name captions."""
+    img_height = 80
+    caption_style = ParagraphStyle(
+        "Caption",
+        parent=styles["Normal"],
+        fontSize=6,
+        leading=6,
+        textColor=colors.black,
+        alignment="CENTER",
+        leftIndent=0,
+        rightIndent=0,
+        spaceAfter=0,
+        spaceBefore=0,
+    )
+
+    image_path_list = sorted(glob.glob(img_dir_path + "/*"))
+
+    if not image_path_list:
+        logger.error(f"No images found in {img_dir_path}")
+        return
+
+    table_data = [
+        [
+            create_sized_img(img_path, img_height),
+            Paragraph(
+                f"<para align=center spaceb=3>{create_filename_caption(img_path)}</para>",
+                caption_style,
+            ),
+        ]
+        for img_path in image_path_list
+    ]
+    img_width = table_data[0][0]._width
+    num_col = int(page_width / img_width)
+    col_width = int(page_width / num_col)
+
+    table_data_rows = [
+        table_data[i : i + num_col] for i in range(0, len(image_path_list), num_col)
+    ]
+
+    table_style = TableStyle(
+        [
+            ("ALIGN", (0, 0), (-1, -1), "CENTER"),
+            ("VALIGN", (0, 0), (-1, -1), "MIDDLE"),
+            ("LEFTPADDING", (0, 0), (-1, -1), 2),
+            ("RIGHTPADDING", (0, 0), (-1, -1), 2),
+            ("TOPPADDING", (0, 0), (-1, -1), 2),
+            ("BOTTOMPADDING", (0, 0), (-1, -1), 5),
+            ("INNERGRID", (0, 0), (-1, -1), 0.25, colors.grey),
+            ("BOX", (0, 0), (-1, -1), 0.25, colors.black),
+        ]
+    )
+    table = Table(table_data_rows, colWidths=col_width)
+    table.setStyle(table_style)
+
+    return table
+
+
+def create_metadata_table(metadata: str) -> Table:
+    """Creates a reportlab Table containing user-inputted metadata."""
+    metadata_dict = json.loads(metadata)
+    metadata_list = list(metadata_dict.items())
+
+    table_style = TableStyle(
+        [
+            ("ALIGN", (0, 0), (-1, -1), "CENTER"),
+            ("VALIGN", (0, 0), (-1, -1), "MIDDLE"),
+            ("LEFTPADDING", (0, 0), (-1, -1), 5),
+            ("RIGHTPADDING", (0, 0), (-1, -1), 5),
+            ("TOPPADDING", (0, 0), (-1, -1), 5),
+            ("BOTTOMPADDING", (0, 0), (-1, -1), 5),
+            ("INNERGRID", (0, 0), (-1, -1), 0.25, colors.grey),
+            ("BOX", (0, 0), (-1, -1), 0.25, colors.black),
+        ]
+    )
+
+    table = Table(metadata_list)
+    table.setStyle(table_style)
+
+    return table
+
+
+def create_pdf(img_dir_path: str, out_path: str, metadata=None) -> None:
+    """Creates a pdf containing images aligned in a grid"""
+    styles = getSampleStyleSheet()
+    pdf = SimpleDocTemplate(
+        out_path,
+        leftMargin=18,
+        rightMargin=18,
+        topMargin=36,
+        bottomMargin=36,
+    )
+    page_width = int(pdf.width)
+
+    flowables = []
+
+    for d in glob.glob(os.path.join(img_dir_path, "*")):
+        title_text = os.path.basename(d) + " Images"
+        title = Paragraph(title_text, styles["Title"])
+        flowables.append(title)
+        flowables.append(Spacer(0, 15))
+
+        mosaic_table = create_mosaic_table(d, page_width, styles)
+        flowables.append(mosaic_table)
+
+        flowables.append(PageBreak())
+
+    if metadata:
+        title = Paragraph("Metadata", styles["Title"])
+        flowables.append(title)
+        flowables.append(Spacer(0, 15))
+
+        metadata_table = create_metadata_table(metadata)
+        flowables.append(metadata_table)
+
+    pdf.build(flowables)
+
+    logger.info("Successfully created pdf")
+
+
+def create_anat_images(layout: BIDSLayout, png_dir: str, downsample=None) -> None:
+    """Creates anatomical mosaic .png files."""
+    anat_layout_kwargs = {
+        "datatype": "anat",
+        "extension": ["nii", "nii.gz"],
+    }
+
+    files = layout.get(**anat_layout_kwargs)
+    anat_png_dir = os.path.join(png_dir, "Anatomical")
+    os.makedirs(anat_png_dir, exist_ok=True)
+
+    for file in files:
+        create_slice_img(file.path, anat_png_dir, layout.root, downsample=downsample)
+
+
+def create_fs_images(fs_dir: str, png_dir: str, downsample=None) -> None:
+    """Creates freesurfer mosaic .png files."""
+    fs_png_dir = os.path.join(png_dir, "Freesurfer")
+    os.makedirs(fs_png_dir, exist_ok=True)
+
+    for file_path in glob.glob(os.path.join(fs_dir, "sub-*/mri/orig/*")):
+        create_slice_img(
+            file_path, fs_png_dir, fs_dir, ds_root=fs_dir, downsample=downsample
+        )
+
+
+def create_mosaic_pdf(
+    dataset: str,
+    out_file: str,
+    anat=True,
+    png_out_dir=None,
+    downsample=None,
+    freesurfer=None,
+    metadata=None,
+) -> None:
+    """Creates a mosaic pdf."""
+    if png_out_dir:
+        png_dir = png_out_dir
+    else:
+        temp_dir_obj = tempfile.TemporaryDirectory()
+        png_dir = temp_dir_obj.name
+
+    layout = BIDSLayout(dataset, validate=False)
+
+    if anat:
+        logger.info(f"Creating anat images in {png_dir}")
+        create_anat_images(layout, png_dir, downsample=downsample)
+    if freesurfer:
+        logger.info(f"Creating freesurfer images in {png_dir}")
+        create_fs_images(freesurfer, png_dir, downsample=downsample)
+
+    logger.info(f"Creating pdf at {out_file}")
+    create_pdf(png_dir, out_file, metadata)
+
+    if not png_out_dir:
+        temp_dir_obj.cleanup()
+
+
+def main():
+    logging.basicConfig(level=logging.INFO)
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("dataset", type=str, help="Path to dataset")
+    parser.add_argument(
+        "-o",
+        "--out-file",
+        type=str,
+        help="Path to output pdf. Defaults to <input dir name>_mosaics.pdf in working directory.",
+    )
+    parser.add_argument(
+        "--png-in-dir",
+        type=str,
+        help="Path to existing directory of .png files, bypassing creation of those from .nii files.",
+    )
+    parser.add_argument(
+        "--png-out-dir",
+        type=str,
+        help="Path to directory to output .png slice images too, instead of creating a temp directory.",
+    )
+    parser.add_argument(
+        "-m",
+        "--metadata",
+        type=str,
+        help="JSON string to include as metadata at the end of the output file.",
+    )
+    parser.add_argument(
+        "--no-anat",
+        action="store_false",
+        dest="anat",
+        help="Do not include anatomical images.",
+    )
+    parser.add_argument(
+        "--freesurfer",
+        type=str,
+        help="Path to freesurfer data.",
+    )
+    parser.add_argument(
+        "--downsample",
+        type=int,
+        help="Factor by which to downsample images.",
+    )
+    parser.add_argument(
+        "--debug",
+        action="store_true",
+        help="Set logging level to DEBUG.",
+    )
+
+    args = parser.parse_args()
+
+    if args.debug:
+        logger.setLevel(logging.DEBUG)
+
+    if args.out_file:
+        out_file = args.out_file
+    else:
+        in_abs = os.path.abspath(args.dataset)
+        out_file = os.path.basename(in_abs) + "_mosaic.pdf"
+
+    if not args.png_in_dir:
+        create_mosaic_pdf(
+            args.dataset,
+            out_file,
+            anat=args.anat,
+            png_out_dir=args.png_out_dir,
+            downsample=args.downsample,
+            freesurfer=args.freesurfer,
+            metadata=args.metadata,
+        )
+    else:
+        logger.info(f"Creating pdf at {out_file}")
+        create_pdf(args.png_in_dir, out_file, args.metadata)
+
+
+if __name__ == "__main__":
+    main()

bids_mosaic-0.0.1/pyproject.toml

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+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "bids-mosaic"
+description = "A BIDS tool for creating PDFs containing slices of nifti images"
+readme = "README.md"
+license = "MIT"
+authors = [
+  { name = "Joseph Wexler", email = "jbwexler@stanford.edu" },
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+]
+version = "0.0.1"
+requires-python = ">=3.10"
+dependencies = [
+    "numpy>=1.24.0",
+    "pybids>=0.16.0",
+    "nilearn>=0.10.0",
+    "nibabel>=5.0.0",
+    "reportlab>=3.6.12",
+    "pillow>=9.3.0",
+    "matplotlib>=3.7.0"
+]
+
+[project.urls]
+Source = "https://github.com/jbwexler/bids-mosaic"
+
+[project.scripts]
+bids-mosaic = "bidsmosaic.mosaic:main"
+
+[tool.setuptools]
+packages = ["bidsmosaic"]

bids_mosaic-0.0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+