Generate neuroglancer compatible 3D pyramids

README.md

@@ -27,7 +27,9 @@ python setup.py install
 
 ## Usage
 
-Argolid can generate Pyramids from a single image or an image collection with a stitching vector provided. It can generate three different kind of pyramids:
+### PyramidGenerator
+
+Argolid can generate 2D Pyramids from a single image or an image collection with a stitching vector provided. It can generate three different kind of pyramids:
 - Neuroglancer compatible Zarr (NG_Zarr)
 - Precomputed Neuroglancer (PCNG)
 - Viv compatible Zarr (Viv)
@@ -43,7 +45,6 @@ output_dir = "/home/samee/axle/data/test_image_ome_zarr"
 min_dim = 1024
 pyr_gen = PyramidGenerartor()
 pyr_gen.generate_from_single_image(input_file, output_dir, min_dim, "NG_Zarr", {0:"mode_max"})
-```
 
 Here is an example of generating a pyramid from a collection of images and a stitching vector.
 ```
@@ -56,4 +57,44 @@ min_dim = 1024
 pyr_gen = PyramidGenerartor()
 pyr_gen.generate_from_image_collection(input_dir, file_pattern, image_name, 
                                         output_dir, min_dim, "Viv", {1:"mean"})
+
+
+
+Argolid provides two main classes for working with volumetric data and generating multi-resolution pyramids:
+
+### VolumeGenerator
+
+The `VolumeGenerator` class is used to create Zarr arrays from image stacks. It handles reading image files, grouping them based on specified criteria, and writing the data into a Zarr array.
+
+Here's an example of how to use `VolumeGenerator`:
+
 ```
+from argolid import VolumeGenerator
+
+source_dir = "/path/to/image/files"
+group_by = "z"  # Group images by z-axis
+file_pattern = "image_{z:d}.tif"
+out_dir = "/path/to/output"
+image_name = "my_volume"
+
+volume_gen = VolumeGenerator(source_dir, group_by, file_pattern, out_dir, image_name)
+volume_gen.generate_volume()
+```
+
+
+
+### PyramidGenerator3D
+
+Here is an example of generating a 3D pyramid from a Zarr array:
+
+
+```
+from argolid import PyramidGenerator3D
+
+zarr_loc_dir = "/path/to/zarr/array"
+base_scale_key = 0
+num_levels = 5
+
+pyramid_gen = PyramidGenerator3D(zarr_loc_dir, base_scale_key)
+pyramid_gen.generate_pyramid(num_levels)
+```

setup.py

@@ -101,7 +101,7 @@ def build_extension(self, ext):
     package_dir={"": "src/python"},
     ext_modules=[CMakeExtension("argolid/libargolid")],
     test_suite="tests",
-    install_requires=["pydantic"],
+    install_requires=["pydantic", "filepattern", "tensorstore", "bfio"],
     zip_safe=False,
     python_requires=">=3.8",
 )

src/python/argolid/__init__.py

@@ -1,4 +1,7 @@
 from .pyramid_generator import PyramidGenerartor, PyramidView, PlateVisualizationMetadata, Downsample
 from .pyramid_compositor import PyramidCompositor
+from .volume_generator import VolumeGenerator, PyramidGenerator3D
+
 from . import _version
-__version__ = _version.get_versions()['version']
+
+__version__ = _version.get_versions()["version"]