Add cellfinder -> brainrender points transformation

.travis.yml

@@ -7,9 +7,6 @@ matrix:
   - os: linux
     python: 3.7
     dist: bionic
-  - os: linux
-    python: 3.8
-    dist: bionic
 before_install:
   - wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
   - bash miniconda.sh -b -p $HOME/miniconda

README.md

@@ -1,2 +1,12 @@
+[![Python Version](https://img.shields.io/pypi/pyversions/neuro.svg)](https://python.org)
+[![PyPI](https://img.shields.io/pypi/v/neuro.svg)](https://pypi.org/project/neuro)
+[![Wheel](https://img.shields.io/pypi/wheel/neuro.svg)](https://pypi.org/project/neuro)
+[![Development Status](https://img.shields.io/pypi/status/neuro.svg)](https://github.com/SainsburyWellcomeCentre/neuro)
+[![Travis](https://img.shields.io/travis/com/SainsburyWellcomeCentre/neuro?label=Travis%20CI)](
+    https://travis-ci.com/SainsburyWellcomeCentre/neuro)
+[![Coverage Status](https://coveralls.io/repos/github/SainsburyWellcomeCentre/neuro/badge.svg?branch=master)](https://coveralls.io/github/SainsburyWellcomeCentre/neuro?branch=master)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
+
+
 # neuro
 Visualisation and analysis of brain imaging data

neuro/points/points_to_brainrender.py

@@ -0,0 +1,110 @@
+"""
+Converts point positions from cellfinder coordinates to brainrender
+
+N.B. This is currently specific to coronal images, with the origin at the most
+caudal, ventral left point. The default is also for 10um voxel spacing.
+"""
+
+import argparse
+import imlib.IO.cells as cells_io
+from imlib.misc import check_positive_float, check_positive_int
+
+
+def run(
+    cells_file,
+    output_filename,
+    pixel_size_x=10,
+    pixel_size_y=10,
+    pixel_size_z=10,
+    max_z=13200,
+    key="df",
+):
+    print(f"Converting file: {cells_file}")
+    cells = cells_io.get_cells(cells_file)
+    cells = cells_io.cells_to_dataframe(cells)
+
+    cells["x"] = cells["x"] * pixel_size_x
+    cells["y"] = cells["y"] * pixel_size_y
+    cells["z"] = cells["z"] * pixel_size_z
+
+    cells.columns = ["z", "y", "x", "type"]
+
+    cells["x"] = max_z - cells["x"]
+
+    print(f"Saving to: {output_filename}")
+    cells.to_hdf(output_filename, key=key, mode="w")
+
+    print("Finished")
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
+    parser.add_argument(
+        dest="cells_file",
+        type=str,
+        help="Cellfinder cells file to be converted",
+    )
+    parser.add_argument(
+        dest="output_filename",
+        type=str,
+        help="Output filename. Should end with '.h5'",
+    )
+
+    parser.add_argument(
+        "-x",
+        "--x-pixel-size",
+        dest="x_pixel_size",
+        type=check_positive_float,
+        default=10,
+        help="Pixel_size that the cells are defined in.",
+    )
+    parser.add_argument(
+        "-y",
+        "--y-pixel-size",
+        dest="y_pixel_size",
+        type=check_positive_float,
+        default=10,
+        help="Pixel_size that the cells are defined in.",
+    )
+    parser.add_argument(
+        "-z",
+        "--z-pixel-size",
+        dest="z_pixel_size",
+        type=check_positive_float,
+        default=10,
+        help="Pixel_size that the cells are defined in.",
+    )
+    parser.add_argument(
+        "--max-z",
+        dest="max_z",
+        type=check_positive_int,
+        default=13200,
+        help="Maximum z extent of the atlas",
+    )
+    parser.add_argument(
+        "--hdf-key",
+        dest="hdf_key",
+        type=str,
+        default="df",
+        help="hdf identifier ",
+    )
+    return parser
+
+
+def main():
+    args = get_parser().parse_args()
+    run(
+        args.cells_file,
+        args.output_filename,
+        pixel_size_x=args.x_pixel_size,
+        pixel_size_y=args.y_pixel_size,
+        pixel_size_z=args.z_pixel_size,
+        max_z=args.max_z,
+        key=args.hdf_key,
+    )
+
+
+if __name__ == "__main__":
+    main()

setup.py

@@ -1,6 +1,6 @@
 from setuptools import setup, find_namespace_packages
 
-requirements = ["brainrender", "napari"]
+requirements = ["brainrender", "napari", "imlib", "pandas"]
 
 
 setup(
@@ -22,7 +22,7 @@
             "coverage<=4.5.4",
         ]
     },
-    python_requires=">=3.6",
+    python_requires=">=3.6, <3.8",
     packages=find_namespace_packages(exclude=("docs", "tests*")),
     include_package_data=True,
     url="https://github.com/SainsburyWellcomeCentre/neuro",
@@ -37,5 +37,11 @@
         "Intended Audience :: Developers",
         "Intended Audience :: Science/Research",
     ],
+    entry_points={
+        "console_scripts": [
+            "points_to_brainrender = "
+            "neuro.points.points_to_brainrender:main",
+        ]
+    },
     zip_safe=False,
 )