nps-cli 0.1.0__tar.gz → 0.1.2__tar.gz

{nps_cli-0.1.0 → nps_cli-0.1.2}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: nps-cli
-Version: 0.1.0
+Version: 0.1.2
 Summary: A simple CLI for sampling point clouds from large volumetric datasets
 Author: Jakob Troidl
 License-Expression: MIT
-Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 Requires-Dist: click
@@ -17,16 +17,18 @@ Requires-Dist: build; extra == "dev"
 Requires-Dist: twine; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 
-# CLI for Point Cloud Sampling
+[![pypi](https://badge.fury.io/py/nps-cli.svg)](https://badge.fury.io/py/nps-cli)
+[![Python Version](https://img.shields.io/pypi/pyversions/nps-cli.svg)](https://pypi.org/project/nps-cli/)
+
+# CLI for Distributed Point Cloud Sampling
 
 ```
-pip install nps
+pip install nps-cli
 ````
 ### Get started
 
-
 ```zsh
-(nps-v2) ➜  nps git:(main) ✗ nps --help
+nps --help
 Usage: nps [OPTIONS]
 
 Options:
@@ -35,7 +37,7 @@ Options:
   --timestamp INTEGER             Optional timestamp for the dataset version
                                   (graphene only).
   --sample_svids                  Sample SVIDs in addition to points (default:
-                                  False).
+                                  False) Graphene only.
   -o, --output-dir DIRECTORY      Output directory.  [default: ./nps_output]
   --worker-type [LocalWorker|LSFWorker|SlurmWorker]
                                   Type of worker to use for sampling.
@@ -47,11 +49,52 @@ Options:
                                   local]
   --fraction FLOAT                Fraction of points to sample [0.0, 1.0].
                                   [default: 0.001]
+  --bbox INTEGER...               Bounding box: begin_x begin_y begin_z
+                                  end_x end_y end_z (in voxels).
   --block-size INTEGER...         Block size in voxels (X Y Z).  [default:
                                   128, 128, 128]
   -h, --help                      Show this message and exit.
 ```
 
+### Example usage
+
 ```bash
 nps --cv-path precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/segmentation
 ```
+
+Sample point clouds within a FlyEM Hemibrain subvolume: 
+
+```bash
+nps --cv-path precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/segmentation --bbox 15347 19712 18606 15859 20224 19118 --fraction 0.01
+```
+
+### Reading Point Clouds
+
+Please refer to the [pocaduck](https://github.com/JaneliaSciComp/pocaduck?tab=readme-ov-file#querying-point-clouds) repo on how to read point clouds from the output directory:
+
+```python
+from pocaduck import Query
+
+# Create a query object
+query = Query(storage_config=<PATH>) # path to folder where nps output is stored
+
+# Get all available labels
+labels = query.get_labels()
+print(f"Available labels: {labels}")
+
+# Get all points for a label (aggregated across all blocks)
+points = query.get_points(label=12345)
+print(f"Retrieved {points.shape[0]} points for label 12345")
+
+# Close the query connection when done
+query.close()
+```
+
+For optimized point cloud reading, consider [this](https://github.com/JaneliaSciComp/pocaduck?tab=readme-ov-file#running-the-optimization-pipeline).
+
+
+### Deploy
+```python
+python -m build
+twine upload dist/*
+```

nps_cli-0.1.2/README.md

@@ -0,0 +1,81 @@
+[![pypi](https://badge.fury.io/py/nps-cli.svg)](https://badge.fury.io/py/nps-cli)
+[![Python Version](https://img.shields.io/pypi/pyversions/nps-cli.svg)](https://pypi.org/project/nps-cli/)
+
+# CLI for Distributed Point Cloud Sampling
+
+```
+pip install nps-cli
+````
+### Get started
+
+```zsh
+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) Graphene only.
+  -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]
+  --bbox INTEGER...               Bounding box: begin_x begin_y begin_z
+                                  end_x end_y end_z (in voxels).
+  --block-size INTEGER...         Block size in voxels (X Y Z).  [default:
+                                  128, 128, 128]
+  -h, --help                      Show this message and exit.
+```
+
+### Example usage
+
+```bash
+nps --cv-path precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/segmentation
+```
+
+Sample point clouds within a FlyEM Hemibrain subvolume: 
+
+```bash
+nps --cv-path precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/segmentation --bbox 15347 19712 18606 15859 20224 19118 --fraction 0.01
+```
+
+### Reading Point Clouds
+
+Please refer to the [pocaduck](https://github.com/JaneliaSciComp/pocaduck?tab=readme-ov-file#querying-point-clouds) repo on how to read point clouds from the output directory:
+
+```python
+from pocaduck import Query
+
+# Create a query object
+query = Query(storage_config=<PATH>) # path to folder where nps output is stored
+
+# Get all available labels
+labels = query.get_labels()
+print(f"Available labels: {labels}")
+
+# Get all points for a label (aggregated across all blocks)
+points = query.get_points(label=12345)
+print(f"Retrieved {points.shape[0]} points for label 12345")
+
+# Close the query connection when done
+query.close()
+```
+
+For optimized point cloud reading, consider [this](https://github.com/JaneliaSciComp/pocaduck?tab=readme-ov-file#running-the-optimization-pipeline).
+
+
+### Deploy
+```python
+python -m build
+twine upload dist/*
+```

{nps_cli-0.1.0 → nps_cli-0.1.2}/nps/main.py

@@ -19,7 +19,8 @@ from volara.workers import LSFWorker, LocalWorker, SlurmWorker
 @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.option('--bbox', nargs=6, type=int, default=None, help='Bounding box: begin_x begin_y begin_z end_x end_y end_z (in voxels).')
+def main(cv_path, mip, timestamp, output_dir, num_workers, cpus_per_worker, queue, fraction, block_size, sample_svids, worker_type, bbox):
 
     click.echo(f"Reading CloudVolume at {cv_path} (mip={mip}, timestamp={timestamp})")
 
@@ -34,8 +35,9 @@ def main(cv_path, mip, timestamp, output_dir, num_workers, cpus_per_worker, queu
         click.echo("Sampling points only (no SVIDs)...")
         svids = None
 
-    if not os.path.exists(output_dir):
-        os.makedirs(output_dir)
+    points_dir = os.path.join(output_dir, 'points')
+    if not os.path.exists(points_dir):
+        os.makedirs(points_dir)
 
     if worker_type == 'LocalWorker':
         click.echo("Using LocalWorker for sampling.")
@@ -47,14 +49,22 @@ def main(cv_path, mip, timestamp, output_dir, num_workers, cpus_per_worker, queu
         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)
 
+    roi = None
+    if bbox is not None:
+        begin = bbox[:3]
+        end = bbox[3:]
+        shape = tuple(e - b for b, e in zip(begin, end))
+        roi = (begin, shape)
+
     task = SamplePoints(
         labels=labels,
         svids=svids,
         block_size=np.array(block_size),
         num_workers=num_workers,
-        out_dir=output_dir,
+        out_dir=points_dir,
         fraction=fraction,
-        worker_config=worker_config
+        worker_config=worker_config,
+        roi=roi,
     )
 
     click.echo("Running task...")

{nps_cli-0.1.0 → nps_cli-0.1.2}/nps_cli.egg-info/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: nps-cli
-Version: 0.1.0
+Version: 0.1.2
 Summary: A simple CLI for sampling point clouds from large volumetric datasets
 Author: Jakob Troidl
 License-Expression: MIT
-Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 Requires-Dist: click
@@ -17,16 +17,18 @@ Requires-Dist: build; extra == "dev"
 Requires-Dist: twine; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 
-# CLI for Point Cloud Sampling
+[![pypi](https://badge.fury.io/py/nps-cli.svg)](https://badge.fury.io/py/nps-cli)
+[![Python Version](https://img.shields.io/pypi/pyversions/nps-cli.svg)](https://pypi.org/project/nps-cli/)
+
+# CLI for Distributed Point Cloud Sampling
 
 ```
-pip install nps
+pip install nps-cli
 ````
 ### Get started
 
-
 ```zsh
-(nps-v2) ➜  nps git:(main) ✗ nps --help
+nps --help
 Usage: nps [OPTIONS]
 
 Options:
@@ -35,7 +37,7 @@ Options:
   --timestamp INTEGER             Optional timestamp for the dataset version
                                   (graphene only).
   --sample_svids                  Sample SVIDs in addition to points (default:
-                                  False).
+                                  False) Graphene only.
   -o, --output-dir DIRECTORY      Output directory.  [default: ./nps_output]
   --worker-type [LocalWorker|LSFWorker|SlurmWorker]
                                   Type of worker to use for sampling.
@@ -47,11 +49,52 @@ Options:
                                   local]
   --fraction FLOAT                Fraction of points to sample [0.0, 1.0].
                                   [default: 0.001]
+  --bbox INTEGER...               Bounding box: begin_x begin_y begin_z
+                                  end_x end_y end_z (in voxels).
   --block-size INTEGER...         Block size in voxels (X Y Z).  [default:
                                   128, 128, 128]
   -h, --help                      Show this message and exit.
 ```
 
+### Example usage
+
 ```bash
 nps --cv-path precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/segmentation
 ```
+
+Sample point clouds within a FlyEM Hemibrain subvolume: 
+
+```bash
+nps --cv-path precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/segmentation --bbox 15347 19712 18606 15859 20224 19118 --fraction 0.01
+```
+
+### Reading Point Clouds
+
+Please refer to the [pocaduck](https://github.com/JaneliaSciComp/pocaduck?tab=readme-ov-file#querying-point-clouds) repo on how to read point clouds from the output directory:
+
+```python
+from pocaduck import Query
+
+# Create a query object
+query = Query(storage_config=<PATH>) # path to folder where nps output is stored
+
+# Get all available labels
+labels = query.get_labels()
+print(f"Available labels: {labels}")
+
+# Get all points for a label (aggregated across all blocks)
+points = query.get_points(label=12345)
+print(f"Retrieved {points.shape[0]} points for label 12345")
+
+# Close the query connection when done
+query.close()
+```
+
+For optimized point cloud reading, consider [this](https://github.com/JaneliaSciComp/pocaduck?tab=readme-ov-file#running-the-optimization-pipeline).
+
+
+### Deploy
+```python
+python -m build
+twine upload dist/*
+```

{nps_cli-0.1.0 → nps_cli-0.1.2}/nps_cli.egg-info/SOURCES.txt

@@ -1,7 +1,6 @@
 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-0.1.0 → nps_cli-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nps-cli"
-version = "0.1.0"
+version = "0.1.2"
 description = "A simple CLI for sampling point clouds from large volumetric datasets"
 readme = { file = "README.md", content-type = "text/markdown" }
 requires-python = ">=3.11"
@@ -17,7 +17,7 @@ dependencies = [
 ]
 
 classifiers = [
-    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
 ]
 
 [project.optional-dependencies]

nps_cli-0.1.0/README.md

@@ -1,38 +0,0 @@
-# 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

@@ -1,5 +0,0 @@
-import yaml
-
-def load_config(path):
-    with open(path, 'r') as f:
-        return yaml.safe_load(f)