nps-cli 0.1.0__tar.gz

nps_cli-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: nps-cli
+Version: 0.1.0
+Summary: A simple CLI for sampling point clouds from large volumetric datasets
+Author: Jakob Troidl
+License-Expression: MIT
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+Requires-Dist: click
+Requires-Dist: volara
+Requires-Dist: pocaduck
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+
+# CLI for Point Cloud Sampling
+
+```
+pip install nps
+````
+### Get started
+
+
+```zsh
+(nps-v2) ➜  nps git:(main) ✗ nps --help
+Usage: nps [OPTIONS]
+
+Options:
+  --cv-path TEXT                  Path to CloudVolume data.  [required]
+  --mip INTEGER                   MIP level to use.  [default: 0]
+  --timestamp INTEGER             Optional timestamp for the dataset version
+                                  (graphene only).
+  --sample_svids                  Sample SVIDs in addition to points (default:
+                                  False).
+  -o, --output-dir DIRECTORY      Output directory.  [default: ./nps_output]
+  --worker-type [LocalWorker|LSFWorker|SlurmWorker]
+                                  Type of worker to use for sampling.
+                                  [default: LocalWorker]
+  --num-workers INTEGER           Number of workers for blockwise sampling.
+                                  [default: 8]
+  --cpus-per-worker INTEGER       Number of CPUs per worker.  [default: 4]
+  --queue TEXT                    Queue name (for LSF backend).  [default:
+                                  local]
+  --fraction FLOAT                Fraction of points to sample [0.0, 1.0].
+                                  [default: 0.001]
+  --block-size INTEGER...         Block size in voxels (X Y Z).  [default:
+                                  128, 128, 128]
+  -h, --help                      Show this message and exit.
+```
+
+```bash
+nps --cv-path precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/segmentation
+```

nps_cli-0.1.0/README.md

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+# CLI for Point Cloud Sampling
+
+```
+pip install nps
+````
+### Get started
+
+
+```zsh
+(nps-v2) ➜  nps git:(main) ✗ nps --help
+Usage: nps [OPTIONS]
+
+Options:
+  --cv-path TEXT                  Path to CloudVolume data.  [required]
+  --mip INTEGER                   MIP level to use.  [default: 0]
+  --timestamp INTEGER             Optional timestamp for the dataset version
+                                  (graphene only).
+  --sample_svids                  Sample SVIDs in addition to points (default:
+                                  False).
+  -o, --output-dir DIRECTORY      Output directory.  [default: ./nps_output]
+  --worker-type [LocalWorker|LSFWorker|SlurmWorker]
+                                  Type of worker to use for sampling.
+                                  [default: LocalWorker]
+  --num-workers INTEGER           Number of workers for blockwise sampling.
+                                  [default: 8]
+  --cpus-per-worker INTEGER       Number of CPUs per worker.  [default: 4]
+  --queue TEXT                    Queue name (for LSF backend).  [default:
+                                  local]
+  --fraction FLOAT                Fraction of points to sample [0.0, 1.0].
+                                  [default: 0.001]
+  --block-size INTEGER...         Block size in voxels (X Y Z).  [default:
+                                  128, 128, 128]
+  -h, --help                      Show this message and exit.
+```
+
+```bash
+nps --cv-path precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/segmentation
+```

nps_cli-0.1.0/nps/config.py

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+import yaml
+
+def load_config(path):
+    with open(path, 'r') as f:
+        return yaml.safe_load(f)

nps_cli-0.1.0/nps/main.py

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+import os
+import numpy as np
+import click
+import time
+
+from nps.blockwise.sample_points import SamplePoints
+from volara.datasets import CloudVolumeWrapper
+from volara.workers import LSFWorker, LocalWorker, SlurmWorker
+
+@click.command(context_settings=dict(help_option_names=['-h', '--help']))
+@click.option('--cv-path', required=True, help='Path to CloudVolume data.')
+@click.option('--mip', default=0, type=int, show_default=True, help='MIP level to use.')
+@click.option('--timestamp', default=int(time.time()), help='Optional timestamp for the dataset version (graphene only).')
+@click.option('--sample_svids', is_flag=True, default=False, help='Sample SVIDs in addition to points (default: False).')
+@click.option('--output-dir', '-o', default='./nps_output', show_default=True, type=click.Path(file_okay=False, writable=True), help='Output directory.')
+@click.option('--worker-type', default='LocalWorker', show_default=True, type=click.Choice(['LocalWorker', 'LSFWorker', 'SlurmWorker'], case_sensitive=True), help='Type of worker to use for sampling.')
+@click.option('--num-workers', default=8, show_default=True, type=int, help='Number of workers for blockwise sampling.')
+@click.option('--cpus-per-worker', default=4, show_default=True, type=int, help='Number of CPUs per worker.')
+@click.option('--queue', default='local', show_default=True, help='Queue name (for LSF backend).')
+@click.option('--fraction', default=0.001, show_default=True, type=float, help='Fraction of points to sample [0.0, 1.0].')
+@click.option('--block-size', nargs=3, type=int, default=(128, 128, 128), show_default=True, help='Block size in voxels (X Y Z).')
+def main(cv_path, mip, timestamp, output_dir, num_workers, cpus_per_worker, queue, fraction, block_size, sample_svids, worker_type):
+
+    click.echo(f"Reading CloudVolume at {cv_path} (mip={mip}, timestamp={timestamp})")
+
+    labels_name = os.path.dirname(output_dir) + "_labels"
+    labels = CloudVolumeWrapper(data_name=labels_name, store=cv_path, mip=mip, timestamp=timestamp)
+
+    if sample_svids:
+        click.echo("Sampling SVIDs in addition to points...")
+        svids_name = os.path.dirname(output_dir) + "_svids"
+        svids = CloudVolumeWrapper(data_name=svids_name, store=cv_path, mip=mip, timestamp=timestamp, agglomerate=False)
+    else:
+        click.echo("Sampling points only (no SVIDs)...")
+        svids = None
+
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+
+    if worker_type == 'LocalWorker':
+        click.echo("Using LocalWorker for sampling.")
+        worker_config = LocalWorker()
+    elif worker_type == 'LSFWorker':
+        click.echo(f"Using LSFWorker with queue '{queue}' and {cpus_per_worker} CPUs per worker.")
+        worker_config = LSFWorker(queue=queue, num_cpus=cpus_per_worker)
+    elif worker_type == 'SlurmWorker':
+        click.echo(f"Using SlurmWorker with queue '{queue}' and {cpus_per_worker} CPUs per worker.")
+        worker_config = SlurmWorker(queue=queue, num_cpus=cpus_per_worker)
+
+    task = SamplePoints(
+        labels=labels,
+        svids=svids,
+        block_size=np.array(block_size),
+        num_workers=num_workers,
+        out_dir=output_dir,
+        fraction=fraction,
+        worker_config=worker_config
+    )
+
+    click.echo("Running task...")
+    task.drop()
+    task.run_blockwise(multiprocessing=True)
+    click.secho("✅ Done!", fg='green')
+
+
+if __name__ == "__main__":
+    main()

nps_cli-0.1.0/nps_cli.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: nps-cli
+Version: 0.1.0
+Summary: A simple CLI for sampling point clouds from large volumetric datasets
+Author: Jakob Troidl
+License-Expression: MIT
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+Requires-Dist: click
+Requires-Dist: volara
+Requires-Dist: pocaduck
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+
+# CLI for Point Cloud Sampling
+
+```
+pip install nps
+````
+### Get started
+
+
+```zsh
+(nps-v2) ➜  nps git:(main) ✗ nps --help
+Usage: nps [OPTIONS]
+
+Options:
+  --cv-path TEXT                  Path to CloudVolume data.  [required]
+  --mip INTEGER                   MIP level to use.  [default: 0]
+  --timestamp INTEGER             Optional timestamp for the dataset version
+                                  (graphene only).
+  --sample_svids                  Sample SVIDs in addition to points (default:
+                                  False).
+  -o, --output-dir DIRECTORY      Output directory.  [default: ./nps_output]
+  --worker-type [LocalWorker|LSFWorker|SlurmWorker]
+                                  Type of worker to use for sampling.
+                                  [default: LocalWorker]
+  --num-workers INTEGER           Number of workers for blockwise sampling.
+                                  [default: 8]
+  --cpus-per-worker INTEGER       Number of CPUs per worker.  [default: 4]
+  --queue TEXT                    Queue name (for LSF backend).  [default:
+                                  local]
+  --fraction FLOAT                Fraction of points to sample [0.0, 1.0].
+                                  [default: 0.001]
+  --block-size INTEGER...         Block size in voxels (X Y Z).  [default:
+                                  128, 128, 128]
+  -h, --help                      Show this message and exit.
+```
+
+```bash
+nps --cv-path precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/segmentation
+```

nps_cli-0.1.0/nps_cli.egg-info/SOURCES.txt

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+README.md
+pyproject.toml
+nps/__init__.py
+nps/config.py
+nps/main.py
+nps_cli.egg-info/PKG-INFO
+nps_cli.egg-info/SOURCES.txt
+nps_cli.egg-info/dependency_links.txt
+nps_cli.egg-info/entry_points.txt
+nps_cli.egg-info/requires.txt
+nps_cli.egg-info/top_level.txt

nps_cli-0.1.0/nps_cli.egg-info/dependency_links.txt

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+

nps_cli-0.1.0/nps_cli.egg-info/entry_points.txt

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+[console_scripts]
+nps = nps.main:main
+
+[volara.blockwise_tasks]
+sample-points = nps.blockwise:SamplePoints

nps_cli-0.1.0/nps_cli.egg-info/requires.txt

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+click
+volara
+pocaduck
+
+[dev]
+pytest
+black
+build
+twine
+ruff

nps_cli-0.1.0/nps_cli.egg-info/top_level.txt

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+nps

nps_cli-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nps-cli"
+version = "0.1.0"
+description = "A simple CLI for sampling point clouds from large volumetric datasets"
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.11"
+license = "MIT"
+authors = [{ name = "Jakob Troidl" }]
+dependencies = [
+    "click",
+    "volara",
+    "pocaduck",
+]
+
+classifiers = [
+    "Programming Language :: Python :: 3",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "black",
+    "build",
+    "twine",
+    "ruff"
+]
+
+[project.entry-points."volara.blockwise_tasks"]
+sample-points = "nps.blockwise:SamplePoints"
+
+[project.scripts]
+nps = "nps.main:main"
+
+[tool.setuptools.packages.find]
+include = ["nps"]
+
+[tool.ruff]
+exclude = ["dist", "build", "nps.egg-info", "volara_logs", "nps_output"]
+line-length = 88
+target-version = "py311"

nps_cli-0.1.0/setup.cfg

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