diff --git a/.github/workflows/init.yml b/.github/workflows/init.yml deleted file mode 100644 index 0336013..0000000 --- a/.github/workflows/init.yml +++ /dev/null @@ -1,52 +0,0 @@ -# Workflow runs only once when the template is first used. -# File can be safely deleted after repo is initialized. -name: Initialize repository -on: - push: - branches: - - main - -jobs: - initialize-package: - name: Initialize the package - if: ${{github.event.repository.name != 'aind-library-template'}} - runs-on: ubuntu-latest - env: - REPO_NAME: ${{ github.event.repository.name }} - GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} - steps: - - name: Checkout - uses: actions/checkout@v3 - - name: Rename package - run: | - pkg_name=$(echo "${REPO_NAME}" | tr - _) - current_description='description = "Prints messages to stdout. Simple boilerplate for libraries."' - new_description='description = "Generated from aind-library-template"' - readme_description='Template for a minimal, basic repository for an AIND library.' - new_readme_description='Generated from aind-library-template' - echo "Package Name ${pkg_name}" - mkdir src/${pkg_name} - touch src/${pkg_name}/__init__.py - echo '"""Init package"""' >> src/${pkg_name}/__init__.py - echo '__version__ = "0.0.0"' >> src/${pkg_name}/__init__.py - sed -i "s/aind_library_template/${pkg_name}/" pyproject.toml - sed -i "s/aind-library-template/${REPO_NAME}/" pyproject.toml - sed -i "s/aind_library_template/${pkg_name}/" doc_template/source/conf.py - sed -i "s/${current_description}/${new_description}/" pyproject.toml - sed -i "/pandas/d" pyproject.toml - sed -i "s/aind-library-template/${REPO_NAME}/" README.md - sed -i "s/${readme_description}/${new_readme_description}/" README.md - - name: Commit changes - uses: EndBug/add-and-commit@v9 - with: - default_author: github_actions - message: "ci: version bump [skip actions]" - add: '["pyproject.toml", "README.md", "src/*", "doc_template/source/conf.py"]' - remove: '["-r src/aind_library_template", "tests/test_message_handler.py"]' - - name: Add first tag - run: | - git tag v0.0.0 - git push origin v0.0.0 - - name: Disable workflow - run: | - gh workflow disable -R $GITHUB_REPOSITORY "${{ github.workflow }}" diff --git a/.github/workflows/tag_and_publish.yml b/.github/workflows/tag_and_publish.yml index 90419da..ca7c3ab 100644 --- a/.github/workflows/tag_and_publish.yml +++ b/.github/workflows/tag_and_publish.yml @@ -3,9 +3,7 @@ on: push: branches: - main -# Remove line 61 to enable automated semantic version bumps. -# Change line 67 from "if: false" to "if: true" to enable PyPI publishing. -# Requires that svc-aindscicomp be added as an admin to repo. + jobs: update_badges: runs-on: ubuntu-latest @@ -16,10 +14,10 @@ jobs: ref: ${{ env.DEFAULT_BRANCH }} fetch-depth: 0 token: ${{ secrets.SERVICE_TOKEN }} - - name: Set up Python 3.8 + - name: Set up Python 3.10 uses: actions/setup-python@v3 with: - python-version: 3.8 + python-version: 3.10 - name: Install dependencies run: | python -m pip install -e .[dev] --no-cache-dir @@ -62,28 +60,6 @@ jobs: add: '["README.md"]' tag: needs: update_badges - if: ${{github.event.repository.name == 'aind-library-template'}} uses: AllenNeuralDynamics/aind-github-actions/.github/workflows/tag.yml@main secrets: SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }} - publish: - needs: tag - if: false - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Pull latest changes - run: git pull origin main - - name: Set up Python 3.8 - uses: actions/setup-python@v2 - with: - python-version: 3.8 - - name: Install dependencies - run: | - pip install --upgrade setuptools wheel twine build - python -m build - twine check dist/* - - name: Publish on PyPI - uses: pypa/gh-action-pypi-publish@release/v1 - with: - password: ${{ secrets.AIND_PYPI_TOKEN }} diff --git a/.github/workflows/test_and_lint.yml b/.github/workflows/test_and_lint.yml index c8d832d..51a8319 100644 --- a/.github/workflows/test_and_lint.yml +++ b/.github/workflows/test_and_lint.yml @@ -10,7 +10,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [ '3.8', '3.9', '3.10' ] + python-version: [ '3.9', '3.10', '3.11' ] steps: - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} diff --git a/README.md b/README.md index 75b35d7..d6d7099 100644 --- a/README.md +++ b/README.md @@ -5,30 +5,62 @@ [![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release) ![Interrogate](https://img.shields.io/badge/interrogate-100.0%25-brightgreen) ![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov) -![Python](https://img.shields.io/badge/python->=3.7-blue?logo=python) +![Python](https://img.shields.io/badge/python->=3.9-blue?logo=python) +## Usage +There are 4 main ways to run a data transformation job: +- from a python script +- from the command line passing in the settings as a json string +- from the command line pointing to a config file +- from the command line with env vars -## Usage - - To use this template, click the green `Use this template` button and `Create new repository`. - - After github initially creates the new repository, please wait an extra minute for the initialization scripts to finish organizing the repo. - - To enable the automatic semantic version increments: in the repository go to `Settings` and `Collaborators and teams`. Click the green `Add people` button. Add `svc-aindscicomp` as an admin. Modify the file in `.github/workflows/tag_and_publish.yml` and remove the if statement in line 10. The semantic version will now be incremented every time a code is committed into the main branch. - - To publish to PyPI, enable semantic versioning and uncomment the publish block in `.github/workflows/tag_and_publish.yml`. The code will now be published to PyPI every time the code is committed into the main branch. - - The `.github/workflows/test_and_lint.yml` file will run automated tests and style checks every time a Pull Request is opened. If the checks are undesired, the `test_and_lint.yml` can be deleted. The strictness of the code coverage level, etc., can be modified by altering the configurations in the `pyproject.toml` file and the `.flake8` file. - -## Installation -To use the software, in the root directory, run +Assuming `output_dir` exists: + +### From python +```python +from aind_data_transformation.ephys.ephys_job import EphysJobSettings, EphysCompressionJob +from pathlib import Path + +input_source = Path("./tests/resources/v0.6.x_neuropixels_multiexp_multistream") +output_dir = Path("output_dir") + +job_settings = EphysJobSettings(input_source=input_source, output_directory=output_dir) +job = EphysCompressionJob(job_settings=job_settings) + +response = job.run_job() +``` + +### From the command line passing in settings as a json str ```bash -pip install -e . +python -m aind_data_transformation.ephys.ephys_job --job-settings '{"input_source":"./tests/resources/v0.6.x_neuropixels_multiexp_multistream","output_directory":"output_dir"}' ``` -To develop the code, run +### From the command line passing in settings via a config file ```bash -pip install -e .[dev] +python -m aind_data_transformation.ephys.ephys_job --config-file configs.json +``` + +### From the command line passing in settings via environment variables +```bash +export TRANSFORMATION_JOB_INPUT_SOURCE="./tests/resources/v0.6.x_neuropixels_multiexp_multistream" +export TRANSFORMATION_JOB_OUTPUT_DIRECTORY="output_dir" +python -m aind_data_transformation.ephys.ephys_job ``` + ## Contributing +The development dependencies can be installed with +```bash +pip install -e .[dev] +``` + +### Adding a new transformation job +Any new job needs a settings class that inherits the BasicJobSettings class. This requires the fields input_source and output_directory and makes it so that the env vars have the TRANSFORMATION_JOB prefix. + +Any new job needs to inherit the GenericEtl class. This requires that the main public method to execute is called `run_job` and returns a JobResponse. + ### Linters and testing There are several libraries used to run linters, check documentation, and run tests. @@ -88,13 +120,3 @@ The table below, from [semantic release](https://github.com/semantic-release/sem | `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release | | `perf(pencil): remove graphiteWidth option`

`BREAKING CHANGE: The graphiteWidth option has been removed.`
`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release
(Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) | -### Documentation -To generate the rst files source files for documentation, run -```bash -sphinx-apidoc -o doc_template/source/ src -``` -Then to create the documentation HTML files, run -```bash -sphinx-build -b html doc_template/source/ doc_template/build/html -``` -More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html). diff --git a/doc_template/source/conf.py b/doc_template/source/conf.py index cef768b..01663d9 100644 --- a/doc_template/source/conf.py +++ b/doc_template/source/conf.py @@ -1,12 +1,15 @@ """Configuration file for the Sphinx documentation builder.""" + # # For the full list of built-in configuration values, see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html +from datetime import date + # -- Path Setup -------------------------------------------------------------- -from os.path import dirname, abspath +from os.path import abspath, dirname from pathlib import Path -from datetime import date + from aind_data_transformation import __version__ as package_version INSTITUTE_NAME = "Allen Institute for Neural Dynamics" diff --git a/pyproject.toml b/pyproject.toml index 7177ac6..ea772c0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta" name = "aind-data-transformation" description = "Generated from aind-library-template" license = {text = "MIT"} -requires-python = ">=3.7" +requires-python = ">=3.9" authors = [ {name = "Allen Institute for Neural Dynamics"} ] @@ -17,10 +17,20 @@ readme = "README.md" dynamic = ["version"] dependencies = [ + 'pydantic>=2.0', + 'pydantic-settings>=2.0', ] [project.optional-dependencies] +ephys = [ + 'spikeinterface[full]>=0.100.0', + 'probeinterface==0.2.21', + 'wavpack-numcodecs>=0.1.3,<=0.1.5', + 'zarr==2.16.1', + 'numcodecs==0.11.0' +] dev = [ + 'aind-data-transformation[ephys]', 'black', 'coverage', 'flake8', @@ -38,7 +48,7 @@ version = {attr = "aind_data_transformation.__version__"} [tool.black] line-length = 79 -target_version = ['py36'] +target_version = ['py39'] exclude = ''' ( diff --git a/src/aind_data_transformation/__init__.py b/src/aind_data_transformation/__init__.py index d0a8547..024d51f 100644 --- a/src/aind_data_transformation/__init__.py +++ b/src/aind_data_transformation/__init__.py @@ -1,2 +1,3 @@ """Init package""" + __version__ = "0.0.0" diff --git a/src/aind_data_transformation/core.py b/src/aind_data_transformation/core.py new file mode 100644 index 0000000..868b4fc --- /dev/null +++ b/src/aind_data_transformation/core.py @@ -0,0 +1,99 @@ +"""Core abstract class that can be used as a template for etl jobs.""" + +import argparse +import json +from abc import ABC, abstractmethod +from pathlib import Path +from typing import Generic, Optional, TypeVar + +from pydantic import BaseModel, ConfigDict, Field +from pydantic_settings import BaseSettings, SettingsConfigDict + + +def get_parser() -> argparse.ArgumentParser: + """ + Get a standard parser that can be used to parse command line args + Returns + ------- + argparse.ArgumentParser + """ + parser = argparse.ArgumentParser() + parser.add_argument( + "-j", + "--job-settings", + required=False, + type=str, + help=( + r""" + Instead of init args the job settings can optionally be passed in + as a json string in the command line. + """ + ), + ) + parser.add_argument( + "-c", + "--config-file", + required=False, + type=Path, + help=( + r""" + Instead of init args the job settings can optionally be loaded from + a config file. + """ + ), + ) + return parser + + +class BasicJobSettings(BaseSettings): + """Model to define Transformation Job Configs""" + + model_config = SettingsConfigDict(env_prefix="TRANSFORMATION_JOB_") + input_source: Path + output_directory: Path + + @classmethod + def from_config_file(cls, config_file_location: Path): + """ + Utility method to create a class from a json file + Parameters + ---------- + config_file_location : Path + Location of json file to read. + + """ + with open(config_file_location, "r") as f: + file_contents = json.load(f) + return cls.model_validate_json(json.dumps(file_contents)) + + +_T = TypeVar("_T", bound=BasicJobSettings) + + +class JobResponse(BaseModel): + """Standard model of a JobResponse.""" + + model_config = ConfigDict(extra="forbid") + status_code: int + message: Optional[str] = Field(None) + data: Optional[str] = Field(None) + + +class GenericEtl(ABC, Generic[_T]): + """A generic etl class. Child classes will need to create a JobSettings + object that is json serializable. Child class will also need to implement + the run_job method, which returns a JobResponse object.""" + + def __init__(self, job_settings: _T): + """ + Class constructor for the GenericEtl class. + Parameters + ---------- + job_settings : _T + Generic type that is bound by the BaseSettings class. + """ + self.job_settings = job_settings + + @abstractmethod + def run_job(self) -> JobResponse: + """Abstract method that needs to be implemented by child classes.""" diff --git a/src/aind_data_transformation/ephys/__init__.py b/src/aind_data_transformation/ephys/__init__.py new file mode 100644 index 0000000..c25a0ae --- /dev/null +++ b/src/aind_data_transformation/ephys/__init__.py @@ -0,0 +1 @@ +"""Package to handle ephys compression job""" diff --git a/src/aind_data_transformation/ephys/ephys_job.py b/src/aind_data_transformation/ephys/ephys_job.py new file mode 100644 index 0000000..725e78c --- /dev/null +++ b/src/aind_data_transformation/ephys/ephys_job.py @@ -0,0 +1,451 @@ +"""Module to handle ephys data compression""" + +import logging +import os +import platform +import shutil +import sys +from datetime import datetime +from pathlib import Path +from typing import Iterator, Literal, Optional, Union + +import numpy as np +import spikeinterface.preprocessing as spre +from numcodecs import Blosc +from pydantic import Field +from spikeinterface import extractors as se +from wavpack_numcodecs import WavPack + +from aind_data_transformation.core import ( + BasicJobSettings, + GenericEtl, + JobResponse, + get_parser, +) +from aind_data_transformation.ephys.models import ( + CompressorName, + ReaderName, + RecordingBlockPrefixes, +) +from aind_data_transformation.ephys.npopto_correction import ( + correct_np_opto_electrode_locations, +) + + +class EphysJobSettings(BasicJobSettings): + """EphysCompressionJob settings.""" + + # reader settings + reader_name: ReaderName = Field( + default=ReaderName.OPENEPHYS, description="Name of reader to use." + ) + # Clip settings + clip_n_frames: int = Field( + default=100, + description="Number of frames to clip the data.", + title="Clip N Frames", + ) + # Compress settings + random_seed: Optional[int] = 0 + compress_write_output_format: Literal["zarr"] = Field( + default="zarr", + description=( + "Output format for compression. Currently, only zarr supported." + ), + title="Write Output Format", + ) + compress_max_windows_filename_len: int = Field( + default=150, + description=( + "Windows OS max filename length is 256. The zarr write will " + "raise an error if it detects that the destination directory has " + "a long name." + ), + title="Compress Max Windows Filename Len", + ) + compressor_name: CompressorName = Field( + default=CompressorName.WAVPACK, + description="Type of compressor to use.", + title="Compressor Name.", + ) + # It will be safer if these kwargs fields were objects with known schemas + compressor_kwargs: dict = Field( + default={"level": 3}, + description="Arguments to be used for the compressor.", + title="Compressor Kwargs", + ) + compress_job_save_kwargs: dict = Field( + default={"n_jobs": -1}, # -1 to use all available cpu cores. + description="Arguments for recording save method.", + title="Compress Job Save Kwargs", + ) + compress_chunk_duration: str = Field( + default="1s", + description="Duration to be used for chunks.", + title="Compress Chunk Duration", + ) + + # Scale settings + scale_num_chunks_per_segment: int = Field( + default=100, + description="Num of chunks per segment to scale.", + title="Scale Num Chunks Per Segment", + ) + scale_chunk_size: int = Field( + default=10000, + description="Chunk size to scale.", + title="Scale Chunk Size", + ) + + +class EphysCompressionJob(GenericEtl[EphysJobSettings]): + """Main class to handle ephys data compression""" + + def _get_read_blocks(self) -> Iterator[dict]: + """ + Uses SpikeInterface to extract read blocks from the input source. + + Returns: + Iterator[dict] + A generator of read blocks. A single read_block is dict with keys: + ('recording', 'experiment_name', 'stream_name') + + """ + nblocks = se.get_neo_num_blocks( + self.job_settings.reader_name.value, self.job_settings.input_source + ) + stream_names, stream_ids = se.get_neo_streams( + self.job_settings.reader_name.value, self.job_settings.input_source + ) + # load first stream to map block_indices to experiment_names + rec_test = se.read_openephys( + self.job_settings.input_source, + block_index=0, + stream_name=stream_names[0], + ) + record_node = list(rec_test.neo_reader.folder_structure.keys())[0] + experiments = rec_test.neo_reader.folder_structure[record_node][ + "experiments" + ] + exp_ids = list(experiments.keys()) + experiment_names = [ + experiments[exp_id]["name"] for exp_id in sorted(exp_ids) + ] + for block_index in range(nblocks): + for stream_name in stream_names: + rec = se.read_openephys( + self.job_settings.input_source, + stream_name=stream_name, + block_index=block_index, + load_sync_timestamps=True, + ) + yield ( + { + "recording": rec, + "experiment_name": experiment_names[block_index], + "stream_name": stream_name, + } + ) + + def _get_streams_to_clip(self) -> Iterator[dict]: + """ + Returns + ------- + Iterator[dict] + A list of dicts with information on which streams to clip. + The dictionary has keys ('data', 'relative_path_name', 'n_chan') + The 'data' is a numpy.memmap object. + + """ + stream_names, stream_ids = se.get_neo_streams( + self.job_settings.reader_name.value, self.job_settings.input_source + ) + for dat_file in self.job_settings.input_source.glob("**/*.dat"): + oe_stream_name = dat_file.parent.name + si_stream_name = [ + stream_name + for stream_name in stream_names + if oe_stream_name in stream_name + ][0] + n_chan = se.read_openephys( + self.job_settings.input_source, + block_index=0, + stream_name=si_stream_name, + ).get_num_channels() + data = np.memmap( + filename=str(dat_file), dtype="int16", order="C", mode="r" + ).reshape(-1, n_chan) + yield { + "data": data, + "relative_path_name": str( + dat_file.relative_to(self.job_settings.input_source) + ), + "n_chan": n_chan, + } + + def _get_compressor(self) -> Union[Blosc, WavPack]: + """ + Utility method to construct a compressor class. + Returns + ------- + Union[Blosc, WavPack] + Either an instantiated Blosc or WavPack class. + + """ + if self.job_settings.compressor_name == CompressorName.BLOSC: + return Blosc(**self.job_settings.compressor_kwargs) + elif self.job_settings.compressor_name == CompressorName.WAVPACK: + return WavPack(**self.job_settings.compressor_kwargs) + else: + # TODO: This is validated during the construction of JobSettings, + # so we can probably just remove this exception. + raise Exception( + f"Unknown compressor. Please select one of " + f"{[c for c in CompressorName]}" + ) + + @staticmethod + def _scale_read_blocks( + read_blocks: Iterator[dict], + random_seed: Optional[int] = None, + num_chunks_per_segment: int = 100, + chunk_size: int = 10000, + ): + """ + Scales read_blocks. A single read_block is dict with keys: + ('recording', 'block_index', 'stream_name') + Parameters + ---------- + read_blocks : Iterator[dict] + A single read_block is dict with keys: + ('recording', 'block_index', 'stream_name') + random_seed : Optional[int] + Optional seed for correct_lsb method. Default is None. + num_chunks_per_segment : int + Default is 100 + chunk_size : int + Default is 10000 + + Returns + ------- + Iterator[dict] + An iterator over read_blocks. A single read_block is dict with keys: + ('scale_recording', 'block_index', 'stream_name') + """ + for read_block in read_blocks: + # We don't need to scale the NI-DAQ recordings + # TODO: Convert this to regex matching? + if RecordingBlockPrefixes.nidaq.value in read_block["stream_name"]: + rec_to_compress = read_block["recording"] + else: + correct_lsb_args = { + "num_chunks_per_segment": num_chunks_per_segment, + "chunk_size": chunk_size, + } + if random_seed is not None: + correct_lsb_args["seed"] = random_seed + rec_to_compress = spre.correct_lsb( + read_block["recording"], **correct_lsb_args + ) + yield ( + { + "scaled_recording": rec_to_compress, + "experiment_name": read_block["experiment_name"], + "stream_name": read_block["stream_name"], + } + ) + + def _copy_and_clip_data( + self, + dst_dir: Path, + stream_gen: Iterator[dict], + ) -> None: + """ + Copies the raw data to a new directory with the .dat files clipped to + just a small number of frames. This allows someone to still use the + spikeinterface api on the clipped data set. + Parameters + ---------- + dst_dir : Path + Desired location for clipped data set + stream_gen : Iterator[dict] + An Iterator where each item is a dictionary with shape, + ('data': memmap(dat file), + 'relative_path_name': path name of raw data to new dir correctly + 'n_chan': number of channels) + Returns + ------- + None + None. Copies clipped *.dat files to a new directory. + + """ + + # first: copy everything except .dat files + patterns_to_ignore = ["*.dat"] + shutil.copytree( + self.job_settings.input_source, + dst_dir, + ignore=shutil.ignore_patterns(*patterns_to_ignore), + ) + # second: copy clipped dat files + for stream in stream_gen: + data = stream["data"] + rel_path_name = stream["relative_path_name"] + n_chan = stream["n_chan"] + dst_raw_file = dst_dir / rel_path_name + dst_data = np.memmap( + filename=dst_raw_file, + dtype="int16", + shape=(self.job_settings.clip_n_frames, n_chan), + order="C", + mode="w+", + ) + dst_data[:] = data[: self.job_settings.clip_n_frames] + + @staticmethod + def _compress_and_write_block( + read_blocks: Iterator[dict], + compressor: Union[WavPack, Blosc], + output_dir: Path, + job_kwargs: dict, + max_windows_filename_len: int, + output_format: str = "zarr", + ) -> None: + """ + Compress and write read_blocks. + + Parameters + ---------- + read_blocks : Iterator[dict] + Either [{'recording', 'block_index', 'stream_name'},...] or + [{'scale_recording', 'block_index', 'stream_name'},...] + compressor : Union[WavPack, Blosc] + output_dir : Path + Output directory to write compressed data + job_kwargs : dict + Recording save job kwargs + max_windows_filename_len : int + Windows OS has a maximum filename length. If the root directory is + deeply nested, the zarr filenames might be too long for Windows. + This is added as an arg, so we can raise better error messages. + output_format : str + Default is zarr + + Returns + ------- + None + Writes data to a folder. + + """ + if job_kwargs["n_jobs"] == -1: + job_kwargs["n_jobs"] = os.cpu_count() + + for read_block in read_blocks: + if "recording" in read_block: + rec = read_block["recording"] + else: + rec = read_block["scaled_recording"] + experiment_name = read_block["experiment_name"] + stream_name = read_block["stream_name"] + zarr_path = output_dir / f"{experiment_name}_{stream_name}.zarr" + if ( + platform.system() == "Windows" + and len(str(zarr_path)) > max_windows_filename_len + ): + raise Exception( + f"File name for zarr path is too long " + f"({len(str(zarr_path))})" + f" and might lead to errors. Use a shorter destination " + f"path." + ) + _ = rec.save( + format=output_format, + folder=zarr_path, + compressor=compressor, + **job_kwargs, + ) + + def _compress_raw_data(self) -> None: + """Compresses ephys data""" + + # Correct NP-opto electrode positions: + # correction is skipped if Neuropix-PXI version > 0.4.0 + # It'd be nice if the original data wasn't modified. + correct_np_opto_electrode_locations(self.job_settings.input_source) + # Clip the data + logging.info("Clipping source data. This may take a minute.") + clipped_data_path = ( + self.job_settings.output_directory / "ecephys_clipped" + ) + streams_to_clip = self._get_streams_to_clip() + self._copy_and_clip_data( + dst_dir=clipped_data_path, + stream_gen=streams_to_clip, + ) + + logging.info("Finished clipping source data.") + + # Compress the data + logging.info("Compressing source data.") + compressed_data_path = ( + self.job_settings.output_directory / "ecephys_compressed" + ) + read_blocks = self._get_read_blocks() + compressor = self._get_compressor() + scaled_read_blocks = self._scale_read_blocks( + read_blocks=read_blocks, + random_seed=self.job_settings.random_seed, + num_chunks_per_segment=( + self.job_settings.scale_num_chunks_per_segment + ), + chunk_size=self.job_settings.scale_chunk_size, + ) + self._compress_and_write_block( + read_blocks=scaled_read_blocks, + compressor=compressor, + max_windows_filename_len=( + self.job_settings.compress_max_windows_filename_len + ), + output_dir=compressed_data_path, + output_format=self.job_settings.compress_write_output_format, + job_kwargs=self.job_settings.compress_job_save_kwargs, + ) + logging.info("Finished compressing source data.") + + return None + + def run_job(self) -> JobResponse: + """ + Main public method to run the compression job + Returns + ------- + JobResponse + Information about the job that can be used for metadata downstream. + + """ + job_start_time = datetime.now() + self._compress_raw_data() + job_end_time = datetime.now() + return JobResponse( + status_code=200, + message=f"Job finished in: {job_end_time-job_start_time}", + data=None, + ) + + +if __name__ == "__main__": + sys_args = sys.argv[1:] + parser = get_parser() + cli_args = parser.parse_args(sys_args) + if cli_args.job_settings is not None: + job_settings = EphysJobSettings.model_validate_json( + cli_args.job_settings + ) + elif cli_args.config_file is not None: + job_settings = EphysJobSettings.from_config_file(cli_args.config_file) + else: + # Construct settings from env vars + job_settings = EphysJobSettings() + job = EphysCompressionJob(job_settings=job_settings) + job_response = job.run_job() + logging.info(job_response.model_dump_json()) diff --git a/src/aind_data_transformation/ephys/models.py b/src/aind_data_transformation/ephys/models.py new file mode 100644 index 0000000..981d86d --- /dev/null +++ b/src/aind_data_transformation/ephys/models.py @@ -0,0 +1,25 @@ +"""Helpful models used in the ephys compression job""" + +from enum import Enum + +from numcodecs import Blosc + + +class ReaderName(str, Enum): + """Enum for readers""" + + OPENEPHYS = "openephys" + + +class CompressorName(str, Enum): + """Enum for compression algorithms a user can select""" + + BLOSC = Blosc.codec_id + WAVPACK = "wavpack" + + +class RecordingBlockPrefixes(str, Enum): + """Enum for types of recording blocks.""" + + neuropix = "Neuropix" + nidaq = "NI-DAQ" diff --git a/src/aind_data_transformation/ephys/npopto_correction.py b/src/aind_data_transformation/ephys/npopto_correction.py new file mode 100644 index 0000000..ba2b4a5 --- /dev/null +++ b/src/aind_data_transformation/ephys/npopto_correction.py @@ -0,0 +1,117 @@ +"""Module to handle np_opto xml settings corrections.""" + +import logging +import xml.etree.ElementTree as ET +from pathlib import Path +from typing import Dict, Tuple, Union + +import numpy as np +from packaging.version import parse + +# geometry properties for NP-opto +X_PITCH = 48 +X_OFFSET = 11 +Y_PITCH = 20 +NUMEL_IN_COL = 192 + + +def get_standard_np_opto_electrode_positions() -> ( + Tuple[Dict[str, str], Dict[str, str]] +): + """ + Get the standard positions for the np_opto electrodes + Returns + ------- + Tuple[Dict[str, str], Dict[str, str]] + """ + npopto_electrode_xpos_arr = [X_OFFSET, X_OFFSET + X_PITCH] * NUMEL_IN_COL + npopto_electrode_ypos_arr = np.concatenate( + [i * np.array([Y_PITCH, Y_PITCH]) for i in range(NUMEL_IN_COL)] + ) + npopto_electrode_xpos = {} + npopto_electrode_ypos = {} + for ch, (xpos, ypos) in enumerate( + zip(npopto_electrode_xpos_arr, npopto_electrode_ypos_arr) + ): + npopto_electrode_xpos[f"CH{ch}"] = str(xpos) + npopto_electrode_ypos[f"CH{ch}"] = str(ypos) + return npopto_electrode_xpos, npopto_electrode_ypos + + +def correct_np_opto_electrode_locations(input_dir: Union[str, Path]) -> None: + """ + + Parameters + ---------- + input_dir : str + Directory location of experimental data root. The xml files located under + this directory will be checked if Neuropix-PXI <= v0.4.0 is used. This + method will copy the original file to settings.xml.wrong and modify + the original file to use the correct np_opto_positions. + + Returns + ------- + None + Modifies the settings.xml file and copies it to a new location. + + """ + # find settings files + input_dir = Path(input_dir) + settings_files = list(input_dir.glob("**/*.xml")) + + ( + npopto_electrode_xpos, + npopto_electrode_ypos, + ) = get_standard_np_opto_electrode_positions() + + for settings_file in settings_files: + # parse xml + tree = ET.parse(str(settings_file)) + root = tree.getroot() + + signal_chain = root.find("SIGNALCHAIN") + neuropix_pxi = None + for processor in signal_chain: + if "PROCESSOR" == processor.tag: + name = processor.attrib["name"] + if "Neuropix-PXI" in name: + neuropix_pxi = processor + break + + if neuropix_pxi is None: + return + neuropix_pxi_version = parse(neuropix_pxi.attrib["libraryVersion"]) + if neuropix_pxi_version > parse("0.4.0"): + # no correction needed for this plugin version + return + + editor = neuropix_pxi.find("EDITOR") + np_probes = editor.findall("NP_PROBE") + + needs_correction = False + for np_probe in np_probes: + if "OPTO" in np_probe.attrib["headstage_part_number"]: + logging.info("Found NP-OPTO!") + needs_correction = True + + # update channel locations + electrode_xpos = np_probe.find("ELECTRODE_XPOS") + electrode_ypos = np_probe.find("ELECTRODE_YPOS") + electrode_xpos.attrib = npopto_electrode_xpos + electrode_ypos.attrib = npopto_electrode_ypos + + settings_file_path = str(settings_file) + if needs_correction: + wrong_settings_file = settings_file.parent / "settings.xml.wrong" + logging.info( + f"Renaming wrong NP-OPTO settings file as " + f"{wrong_settings_file}" + ) + settings_file.rename(wrong_settings_file) + logging.info( + f"Saving correct NP-OPTO settings file as " + f"{settings_file_path}" + ) + tree.write(settings_file_path) + else: + logging.info(f"No NP-OPTO probes found in {settings_file_path}") diff --git a/tests/resources/core_example_settings/settings.json b/tests/resources/core_example_settings/settings.json new file mode 100644 index 0000000..b56942a --- /dev/null +++ b/tests/resources/core_example_settings/settings.json @@ -0,0 +1,5 @@ +{ + "input_source": "some_input_dir", + "output_directory": "some_output_dir", + "param": 2 +} \ No newline at end of file diff --git a/tests/resources/np_opto_corrections/settings_2022_07/settings.xml b/tests/resources/np_opto_corrections/settings_2022_07/settings.xml new file mode 100644 index 0000000..2f33189 --- /dev/null +++ b/tests/resources/np_opto_corrections/settings_2022_07/settings.xml @@ -0,0 +1,426 @@ + + + + + 0.6.0 + 8 + 14 Jul 2022 13:55:57 + Windows 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/resources/np_opto_corrections/settings_2023_04/settings.xml b/tests/resources/np_opto_corrections/settings_2023_04/settings.xml new file mode 100644 index 0000000..1d564d7 --- /dev/null +++ b/tests/resources/np_opto_corrections/settings_2023_04/settings.xml @@ -0,0 +1,459 @@ + + + + + 0.6.2 + 8 + 3 Apr 2023 18:17:07 + Windows 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/resources/np_opto_corrections/settings_2024_01/settings.xml b/tests/resources/np_opto_corrections/settings_2024_01/settings.xml new file mode 100644 index 0000000..166ee58 --- /dev/null +++ b/tests/resources/np_opto_corrections/settings_2024_01/settings.xml @@ -0,0 +1,676 @@ + + + + + 0.6.6 + 8 + 12 Jan 2024 15:27:46 + Windows 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/resources/np_opto_corrections/settings_altered_no_pxi/settings.xml b/tests/resources/np_opto_corrections/settings_altered_no_pxi/settings.xml new file mode 100644 index 0000000..23b2f17 --- /dev/null +++ b/tests/resources/np_opto_corrections/settings_altered_no_pxi/settings.xml @@ -0,0 +1,703 @@ + + + + + 0.6.6 + 8 + 1 Nov 2023 16:48:18 + Windows 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/resources/np_opto_corrections/standard_positions.json b/tests/resources/np_opto_corrections/standard_positions.json new file mode 100644 index 0000000..00a1404 --- /dev/null +++ b/tests/resources/np_opto_corrections/standard_positions.json @@ -0,0 +1,774 @@ +[ + { + "CH0": "11", + "CH1": "59", + "CH2": "11", + "CH3": "59", + "CH4": "11", + "CH5": "59", + "CH6": "11", + "CH7": "59", + "CH8": "11", + "CH9": "59", + "CH10": "11", + "CH11": "59", + "CH12": "11", + "CH13": "59", + "CH14": "11", + "CH15": "59", + "CH16": "11", + "CH17": "59", + "CH18": "11", + "CH19": "59", + "CH20": "11", + "CH21": "59", + "CH22": "11", + "CH23": "59", + "CH24": "11", + "CH25": "59", + "CH26": "11", + "CH27": "59", + "CH28": "11", + "CH29": "59", + "CH30": "11", + "CH31": "59", + "CH32": "11", + "CH33": "59", + "CH34": "11", + "CH35": "59", + "CH36": "11", + "CH37": "59", + "CH38": "11", + "CH39": "59", + "CH40": "11", + "CH41": "59", + "CH42": "11", + "CH43": 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{ + "channel_name": "CH363", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH364", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH365", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH366", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH367", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH368", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH369", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH370", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH371", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH372", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH373", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH374", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH375", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH376", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH377", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH378", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH379", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH380", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH381", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH382", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH383", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + }, + { + "channel_name": "CH384", + "description": "Neuropixels electrode", + "identifier": "", + "history": "Neuropix-PXI -> Merger -> Record Node", + "bit_volts": 0.1949999928474426, + "units": "" + } + ] + }, + { + "folder_name": "NI-DAQmx-103.PXIe-6341/", + "sample_rate": 30000.0, + "source_processor_name": "NI-DAQmx", + "source_processor_id": 103, + "stream_name": "PXIe-6341", + "recorded_processor": "Record Node", + "recorded_processor_id": 101, + "num_channels": 8, + "channels": [ + { + "channel_name": "AI0", + "description": "Analog Input channel from a NIDAQ device", + "identifier": "", + "history": "NI-DAQmx -> Merger -> Record Node", + "bit_volts": 0.0003051850944757462, + "units": "" + }, + { + "channel_name": "AI1", + "description": "Analog Input channel from a NIDAQ device", + "identifier": "", + "history": "NI-DAQmx -> Merger -> Record Node", + "bit_volts": 0.0003051850944757462, + "units": "" + }, + { + "channel_name": "AI2", + "description": "Analog Input channel from a NIDAQ device", + "identifier": "", + "history": "NI-DAQmx -> Merger -> Record Node", + "bit_volts": 0.0003051850944757462, + "units": "" + }, + { + "channel_name": "AI3", + "description": "Analog Input channel from a NIDAQ device", + "identifier": "", + "history": "NI-DAQmx -> Merger -> Record Node", + "bit_volts": 0.0003051850944757462, + "units": "" + }, + { + "channel_name": "AI4", + "description": "Analog Input channel from a NIDAQ device", + "identifier": "", + "history": "NI-DAQmx -> Merger -> Record Node", + "bit_volts": 0.0003051850944757462, + "units": "" + }, + { + "channel_name": "AI5", + "description": "Analog Input channel from a NIDAQ device", + "identifier": "", + "history": "NI-DAQmx -> Merger -> Record Node", + "bit_volts": 0.0003051850944757462, + "units": "" + }, + { + "channel_name": "AI6", + "description": "Analog Input channel from a NIDAQ device", + "identifier": "", + "history": "NI-DAQmx -> Merger -> Record Node", + "bit_volts": 0.0003051850944757462, + "units": "" + }, + { + "channel_name": "AI7", + "description": "Analog Input channel from a NIDAQ device", + "identifier": "", + "history": "NI-DAQmx -> Merger -> Record Node", + "bit_volts": 0.0003051850944757462, + "units": "" + } + ] + } + ], + "events": [ + { + "folder_name": "Neuropix-PXI-100.ProbeB/TTL/", + "channel_name": "Neuropixels PXI Sync", + "description": "Status of SMA sync line on PXI card", + "identifier": "neuropixels.sync", + "sample_rate": 30000.0, + "type": "int16", + "source_processor": "Neuropix-PXI", + "stream_name": "ProbeB", + "initial_state": 0 + }, + { + "folder_name": "Neuropix-PXI-100.ProbeC/TTL/", + "channel_name": "Neuropixels PXI Sync", + "description": "Status of SMA sync line on PXI card", + "identifier": "neuropixels.sync", + "sample_rate": 30000.0, + "type": "int16", + "source_processor": "Neuropix-PXI", + "stream_name": "ProbeC", + "initial_state": 0 + }, + { + "folder_name": "NI-DAQmx-103.PXIe-6341/TTL/", + "channel_name": "PXIe-6341Digital Input Line", + "description": "Digital Line from a NIDAQ device containing 8 inputs", + "identifier": "identifier", + "sample_rate": 30000.0, + "type": "int16", + "source_processor": "NI-DAQmx", + "stream_name": "PXIe-6341", + "initial_state": 0 + }, + { + "folder_name": "MessageCenter/", + "channel_name": "Messages", + "description": "Broadcasts messages from the MessageCenter", + "identifier": "messagecenter.events", + "sample_rate": 30000.0, + "type": "string", + "source_processor": "Message Center", + "stream_name": "ProbeB" + } + ], + "spikes": [] + } \ No newline at end of file diff --git a/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/experiment6/recording1/sync_messages.txt b/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/experiment6/recording1/sync_messages.txt new file mode 100644 index 0000000..9e0c6e2 --- /dev/null +++ b/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/experiment6/recording1/sync_messages.txt @@ -0,0 +1,4 @@ +Software Time (milliseconds since midnight Jan 1st 1970 UTC): 1651602328909 +Start Time for Neuropix-PXI (100) - ProbeB @ 30000 Hz: 255285 +Start Time for Neuropix-PXI (100) - ProbeC @ 30000 Hz: 255667 +Start Time for NI-DAQmx (103) - PXIe-6341 @ 30000 Hz: 265001 diff --git a/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings.xml b/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings.xml new file mode 100644 index 0000000..51d287b --- /dev/null +++ b/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings.xml @@ -0,0 +1,752 @@ + + + + + 0.6.0 + 8 + 3 May 2022 10:52:24 + Windows 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings_3.xml b/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings_3.xml new file mode 100644 index 0000000..2737d7b --- /dev/null +++ b/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings_3.xml @@ -0,0 +1,752 @@ + + + + + 0.6.0 + 8 + 3 May 2022 11:09:55 + Windows 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings_6.xml b/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings_6.xml new file mode 100644 index 0000000..4ff8157 --- /dev/null +++ b/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings_6.xml @@ -0,0 +1,752 @@ + + + + + 0.6.0 + 8 + 3 May 2022 11:25:28 + Windows 10 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + diff --git a/tests/test_core.py b/tests/test_core.py new file mode 100644 index 0000000..8893bdc --- /dev/null +++ b/tests/test_core.py @@ -0,0 +1,96 @@ +"""Module to test core and models module""" + +import os +import unittest +from pathlib import Path +from unittest.mock import patch + +from aind_data_transformation.core import ( + BasicJobSettings, + GenericEtl, + JobResponse, + get_parser, +) + +TEST_DIR = Path(os.path.dirname(os.path.realpath(__file__))) / "resources" +SETTINGS_FILE_PATH = TEST_DIR / "core_example_settings" / "settings.json" + + +class ExampleJobSettings(BasicJobSettings): + """Create an example job settings class""" + + param: int = 1 + + +class ExampleJob(GenericEtl[ExampleJobSettings]): + """Create an example etl job class""" + + def run_job(self) -> JobResponse: + """Required method for all Etl Jobs""" + return JobResponse( + status_code=200, + data=None, + message=f"Param {self.job_settings.param}", + ) + + +class TestExampleEtl(unittest.TestCase): + """Module to test core etl methods""" + + EXAMPLE_ENV_VAR1 = { + "TRANSFORMATION_JOB_PARAM": "2", + "TRANSFORMATION_JOB_INPUT_SOURCE": "some_input_dir", + "TRANSFORMATION_JOB_OUTPUT_DIRECTORY": "some_output_dir", + } + + @classmethod + def setUpClass(cls) -> None: + """Set up tests with basic job settings and etl job""" + basic_settings = ExampleJobSettings( + param=2, + input_source=Path("some_input_dir"), + output_directory=Path("some_output_dir"), + ) + cls.basic_settings = basic_settings + cls.basic_job = ExampleJob(job_settings=basic_settings) + + def test_load_cli_args_json_str(self): + """Tests loading json string defined in command line args""" + job_settings_json = self.basic_settings.model_dump_json() + parser = get_parser() + cli_args = ["--job-settings", job_settings_json] + parsed_args = parser.parse_args(cli_args) + loaded_job_settings = ExampleJobSettings.model_validate_json( + parsed_args.job_settings + ) + self.assertEqual(self.basic_settings, loaded_job_settings) + + def test_load_cli_args_file_path(self): + """Tests loading config file defined in command line args""" + parser = get_parser() + cli_args = ["--config-file", str(SETTINGS_FILE_PATH)] + parsed_args = parser.parse_args(cli_args) + loaded_job_settings = ExampleJobSettings.from_config_file( + parsed_args.config_file + ) + self.assertEqual(self.basic_settings, loaded_job_settings) + + @patch.dict(os.environ, EXAMPLE_ENV_VAR1, clear=True) + def test_load_env_vars(self): + """Tests loading job settings through env vars""" + job_settings = ExampleJobSettings() + + self.assertEqual(self.basic_settings, job_settings) + + @patch.dict(os.environ, EXAMPLE_ENV_VAR1, clear=True) + def test_run_job(self): + """Tests the run_job method in the ExampleEtl""" + response = self.basic_job.run_job() + expected_response = JobResponse( + status_code=200, data=None, message="Param 2" + ) + self.assertEqual(response, expected_response) + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/test_ephys_job.py b/tests/test_ephys_job.py new file mode 100644 index 0000000..287072a --- /dev/null +++ b/tests/test_ephys_job.py @@ -0,0 +1,1206 @@ +"""Tests for the ephys package""" + +import json +import os +import unittest +from datetime import datetime +from pathlib import Path +from unittest.mock import MagicMock, call, patch + +from numcodecs import Blosc +from wavpack_numcodecs import WavPack + +from aind_data_transformation.core import JobResponse +from aind_data_transformation.ephys.ephys_job import ( + EphysCompressionJob, + EphysJobSettings, +) +from aind_data_transformation.ephys.models import CompressorName +from aind_data_transformation.ephys.npopto_correction import ( + correct_np_opto_electrode_locations, + get_standard_np_opto_electrode_positions, +) + +TEST_DIR = Path(os.path.dirname(os.path.realpath(__file__))) / "resources" +DATA_DIR = TEST_DIR / "v0.6.x_neuropixels_multiexp_multistream" +NP_OPTO_CORRECT_DIR = TEST_DIR / "np_opto_corrections" + + +class TestEphysJob(unittest.TestCase): + """Tests for ephys_job module""" + + @classmethod + def setUpClass(cls): + """Setup basic job settings and job that can be used across tests""" + basic_job_settings = EphysJobSettings( + input_source=DATA_DIR, + output_directory=Path("output_dir"), + compress_job_save_kwargs={"n_jobs": 1}, + ) + cls.basic_job_settings = basic_job_settings + cls.basic_job = EphysCompressionJob(job_settings=basic_job_settings) + + @patch("warnings.warn") + def test_get_compressor_default(self, _: MagicMock): + """Tests _get_compressor_default method with default settings.""" + compressor = self.basic_job._get_compressor() + expected_default = WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ) + self.assertEqual(expected_default, compressor) + + @patch("warnings.warn") + def test_get_compressor_wavpack(self, _: MagicMock): + """Tests _get_compressor_default method with WavPack settings.""" + compressor_kwargs = { + "level": 4, + } + settings = EphysJobSettings( + input_source=Path("input_dir"), + output_directory=Path("output_dir"), + compressor_name=CompressorName.WAVPACK, + compressor_kwargs=compressor_kwargs, + ) + etl_job = EphysCompressionJob(job_settings=settings) + compressor = etl_job._get_compressor() + expected_compressor = WavPack( + bps=0, + dynamic_noise_shaping=True, + level=4, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ) + self.assertEqual(expected_compressor, compressor) + + def test_get_compressor_blosc(self): + """Tests _get_compressor_default method with Blosc settings.""" + compressor_kwargs = { + "clevel": 4, + } + settings = EphysJobSettings( + input_source=Path("input_dir"), + output_directory=Path("output_dir"), + compressor_name=CompressorName.BLOSC, + compressor_kwargs=compressor_kwargs, + ) + etl_job = EphysCompressionJob(job_settings=settings) + compressor = etl_job._get_compressor() + expected_compressor = Blosc(clevel=4) + self.assertEqual(expected_compressor, compressor) + + def test_get_compressor_error(self): + """Tests _get_compressor_default method with unknown compressor.""" + + etl_job = EphysCompressionJob( + job_settings=EphysJobSettings.model_construct( + compressor_name="UNKNOWN" + ) + ) + with self.assertRaises(Exception) as e: + etl_job._get_compressor() + + expected_error_message = ( + "Unknown compressor. Please select one of " + "[, " + "]", + ) + self.assertEqual(expected_error_message, e.exception.args) + + def test_get_read_blocks(self): + """Tests _get_read_blocks method""" + read_blocks = self.basic_job._get_read_blocks() + # Instead of constructing OpenEphysBinaryRecordingExtractor to + # compare against, we can just compare the repr of the classes + read_blocks_repr = [] + for read_block in read_blocks: + copied_read_block = read_block + copied_read_block["recording"] = repr(read_block["recording"]) + read_blocks_repr.append(copied_read_block) + extractor_str_1 = ( + "OpenEphysBinaryRecordingExtractor: 8 channels - 30.0kHz " + "- 1 segments - 100 samples \n" + " 0.00s (3.33 ms) - int16 dtype " + "- 1.56 KiB" + ) + extractor_str_2 = ( + "OpenEphysBinaryRecordingExtractor: 384 channels - 30.0kHz " + "- 1 segments - 100 samples \n" + " 0.00s (3.33 ms) - int16 dtype " + "- 75.00 KiB" + ) + expected_read_blocks = [ + { + "recording": extractor_str_1, + "experiment_name": "experiment1", + "stream_name": "Record Node 101#NI-DAQmx-103.PXIe-6341", + }, + { + "recording": extractor_str_2, + "experiment_name": "experiment1", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeB", + }, + { + "recording": extractor_str_2, + "experiment_name": "experiment1", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeC", + }, + { + "recording": extractor_str_1, + "experiment_name": "experiment3", + "stream_name": "Record Node 101#NI-DAQmx-103.PXIe-6341", + }, + { + "recording": extractor_str_2, + "experiment_name": "experiment3", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeB", + }, + { + "recording": extractor_str_2, + "experiment_name": "experiment3", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeC", + }, + { + "recording": extractor_str_1, + "experiment_name": "experiment6", + "stream_name": "Record Node 101#NI-DAQmx-103.PXIe-6341", + }, + { + "recording": extractor_str_2, + "experiment_name": "experiment6", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeB", + }, + { + "recording": extractor_str_2, + "experiment_name": "experiment6", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeC", + }, + ] + expected_scaled_read_blocks_str = set( + [json.dumps(o) for o in expected_read_blocks] + ) + read_blocks_repr_str = set([json.dumps(o) for o in read_blocks_repr]) + self.assertEqual(expected_scaled_read_blocks_str, read_blocks_repr_str) + + def test_scale_read_blocks(self): + """Tests _scale_read_blocks method""" + read_blocks = self.basic_job._get_read_blocks() + scaled_read_blocks = self.basic_job._scale_read_blocks( + read_blocks=read_blocks, + random_seed=0, + num_chunks_per_segment=10, + chunk_size=50, + ) + # Instead of constructing ScaledRecording classes to + # compare against, we can just compare the repr of the classes + scaled_read_blocks_repr = [] + for read_block in scaled_read_blocks: + copied_read_block = read_block + copied_read_block["scaled_recording"] = repr( + read_block["scaled_recording"] + ) + scaled_read_blocks_repr.append(copied_read_block) + + extractor_str_1 = ( + "OpenEphysBinaryRecordingExtractor: 8 channels - 30.0kHz " + "- 1 segments - 100 samples \n" + " 0.00s (3.33 ms) - int16 dtype " + "- 1.56 KiB" + ) + extractor_str_2 = ( + "ScaleRecording: 384 channels - 30.0kHz - 1 segments " + "- 100 samples - 0.00s (3.33 ms) - int16 dtype \n" + " 75.00 KiB" + ) + + expected_scaled_read_blocks = [ + { + "scaled_recording": extractor_str_1, + "experiment_name": "experiment1", + "stream_name": "Record Node 101#NI-DAQmx-103.PXIe-6341", + }, + { + "scaled_recording": extractor_str_2, + "experiment_name": "experiment1", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeB", + }, + { + "scaled_recording": extractor_str_2, + "experiment_name": "experiment1", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeC", + }, + { + "scaled_recording": extractor_str_1, + "experiment_name": "experiment3", + "stream_name": "Record Node 101#NI-DAQmx-103.PXIe-6341", + }, + { + "scaled_recording": extractor_str_2, + "experiment_name": "experiment3", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeB", + }, + { + "scaled_recording": extractor_str_2, + "experiment_name": "experiment3", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeC", + }, + { + "scaled_recording": extractor_str_1, + "experiment_name": "experiment6", + "stream_name": "Record Node 101#NI-DAQmx-103.PXIe-6341", + }, + { + "scaled_recording": extractor_str_2, + "experiment_name": "experiment6", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeB", + }, + { + "scaled_recording": extractor_str_2, + "experiment_name": "experiment6", + "stream_name": "Record Node 101#Neuropix-PXI-100.ProbeC", + }, + ] + expected_scaled_read_blocks_str = set( + [json.dumps(o) for o in expected_scaled_read_blocks] + ) + scaled_read_blocks_repr_str = set( + [json.dumps(o) for o in scaled_read_blocks_repr] + ) + self.assertEqual( + expected_scaled_read_blocks_str, scaled_read_blocks_repr_str + ) + + def test_get_streams_to_clip(self): + """Tests _get_streams_to_clip method""" + streams_to_clip = self.basic_job._get_streams_to_clip() + # TODO: If we want finer granularity, we can compare the numpy.memmap + # directly instead of just checking their shape + streams_to_clip_just_shape = [] + for stream_to_clip in streams_to_clip: + stream_to_clip_copy = { + "relative_path_name": stream_to_clip["relative_path_name"], + "n_chan": stream_to_clip["n_chan"], + "data": stream_to_clip["data"].shape, + } + streams_to_clip_just_shape.append(stream_to_clip_copy) + + def base_path(num: int) -> Path: + """Utility method to construct expected output base paths""" + return ( + Path("Record Node 101") + / f"experiment{num}" + / "recording1" + / "continuous" + ) + + expected_output = [ + { + "relative_path_name": str( + base_path(1) / "Neuropix-PXI-100.ProbeB" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + { + "relative_path_name": str( + base_path(1) / "Neuropix-PXI-100.ProbeC" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + { + "relative_path_name": str( + base_path(1) / "NI-DAQmx-103.PXIe-6341" / "continuous.dat" + ), + "n_chan": 8, + "data": (100, 8), + }, + { + "relative_path_name": str( + base_path(6) / "Neuropix-PXI-100.ProbeB" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + { + "relative_path_name": str( + base_path(6) / "Neuropix-PXI-100.ProbeC" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + { + "relative_path_name": str( + base_path(6) / "NI-DAQmx-103.PXIe-6341" / "continuous.dat" + ), + "n_chan": 8, + "data": (100, 8), + }, + { + "relative_path_name": str( + base_path(3) / "NI-DAQmx-103.PXIe-6341" / "continuous.dat" + ), + "n_chan": 8, + "data": (100, 8), + }, + { + "relative_path_name": str( + base_path(3) / "Neuropix-PXI-100.ProbeB" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + { + "relative_path_name": str( + base_path(3) / "Neuropix-PXI-100.ProbeC" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + ] + expected_output_str = set([json.dumps(o) for o in expected_output]) + streams_to_clip_just_shape_str = set( + [json.dumps(o) for o in streams_to_clip_just_shape] + ) + self.assertEqual(expected_output_str, streams_to_clip_just_shape_str) + + @patch("shutil.copytree") + @patch("shutil.ignore_patterns") + @patch("numpy.memmap") + def test_copy_and_clip_data( + self, + mock_memmap: MagicMock, + mock_ignore_patterns: MagicMock, + mock_copy_tree: MagicMock, + ): + """Tests _copy_and_clip_data method""" + mock_ignore_patterns.return_value = ["*.dat"] + + def base_path(num: int) -> Path: + """Utility method to construct expected output base paths""" + return ( + Path("Record Node 101") + / f"experiment{num}" + / "recording1" + / "continuous" + ) + + expected_output = [ + { + "relative_path_name": str( + base_path(1) / "Neuropix-PXI-100.ProbeB" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + { + "relative_path_name": str( + base_path(1) / "Neuropix-PXI-100.ProbeC" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + { + "relative_path_name": str( + base_path(1) / "NI-DAQmx-103.PXIe-6341" / "continuous.dat" + ), + "n_chan": 8, + "data": (100, 8), + }, + { + "relative_path_name": str( + base_path(6) / "Neuropix-PXI-100.ProbeB" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + { + "relative_path_name": str( + base_path(6) / "Neuropix-PXI-100.ProbeC" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + { + "relative_path_name": str( + base_path(6) / "NI-DAQmx-103.PXIe-6341" / "continuous.dat" + ), + "n_chan": 8, + "data": (100, 8), + }, + { + "relative_path_name": str( + base_path(3) / "NI-DAQmx-103.PXIe-6341" / "continuous.dat" + ), + "n_chan": 8, + "data": (100, 8), + }, + { + "relative_path_name": str( + base_path(3) / "Neuropix-PXI-100.ProbeB" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + { + "relative_path_name": str( + base_path(3) / "Neuropix-PXI-100.ProbeC" / "continuous.dat" + ), + "n_chan": 384, + "data": (100, 384), + }, + ] + expected_memmap_calls = [] + for foobar in expected_output: + expected_memmap_calls.append( + call( + filename=Path(foobar["relative_path_name"]), + dtype="int16", + shape=foobar["data"], + order="C", + mode="w+", + ) + ) + expected_memmap_calls.append( + call().__setitem__(slice(None, None, None), foobar["data"]) + ) + self.basic_job._copy_and_clip_data( + dst_dir=Path("."), stream_gen=expected_output + ) + mock_ignore_patterns.assert_called_once_with("*.dat") + mock_copy_tree.assert_called_once_with( + DATA_DIR, Path("."), ignore=["*.dat"] + ) + mock_memmap.assert_has_calls(expected_memmap_calls) + + @patch("warnings.warn") + @patch( + "spikeinterface.extractors.neoextractors.openephys" + ".OpenEphysBinaryRecordingExtractor.save" + ) + @patch("spikeinterface.preprocessing.normalize_scale.ScaleRecording.save") + def test_compress_and_write_scaled_blocks( + self, + mock_scale_save: MagicMock, + mock_bin_save: MagicMock, + _: MagicMock, + ): + """Tests _compress_and_write_block method with scaled rec""" + read_blocks = self.basic_job._get_read_blocks() + scaled_read_blocks = self.basic_job._scale_read_blocks( + read_blocks=read_blocks, + random_seed=0, + num_chunks_per_segment=10, + chunk_size=50, + ) + compressor = self.basic_job._get_compressor() + max_windows_filename_len = ( + self.basic_job.job_settings.compress_max_windows_filename_len + ) + output_dir = ( + self.basic_job.job_settings.output_directory / "compressed" + ) + output_format = ( + self.basic_job.job_settings.compress_write_output_format + ) + job_kwargs = self.basic_job.job_settings.compress_job_save_kwargs + self.basic_job._compress_and_write_block( + read_blocks=scaled_read_blocks, + compressor=compressor, + max_windows_filename_len=max_windows_filename_len, + output_dir=output_dir, + output_format=output_format, + job_kwargs=job_kwargs, + ) + mock_bin_save.assert_has_calls( + [ + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment1_Record Node 101#NI-DAQmx-103" + ".PXIe-6341.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment3_Record Node 101#NI-DAQmx-103" + ".PXIe-6341.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment6_Record Node 101#NI-DAQmx-103" + ".PXIe-6341.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + ] + ) + mock_scale_save.assert_has_calls( + [ + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment1_Record Node 101#Neuropix-PXI-100" + ".ProbeB.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment1_Record Node 101#Neuropix-PXI-100" + ".ProbeC.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment3_Record Node 101#Neuropix-PXI-100" + ".ProbeB.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment3_Record Node 101#Neuropix-PXI-100" + ".ProbeC.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment6_Record Node 101#Neuropix-PXI-100" + ".ProbeB.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment6_Record Node 101#Neuropix-PXI-100" + ".ProbeC.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + ] + ) + + @patch("warnings.warn") + @patch( + "spikeinterface.extractors.neoextractors.openephys" + ".OpenEphysBinaryRecordingExtractor.save" + ) + def test_compress_and_write_read_blocks( + self, + mock_bin_save: MagicMock, + _: MagicMock, + ): + """Tests _compress_and_write_block method with raw rec""" + read_blocks = self.basic_job._get_read_blocks() + compressor = self.basic_job._get_compressor() + max_windows_filename_len = ( + self.basic_job.job_settings.compress_max_windows_filename_len + ) + output_dir = ( + self.basic_job.job_settings.output_directory / "compressed" + ) + output_format = ( + self.basic_job.job_settings.compress_write_output_format + ) + job_kwargs = self.basic_job.job_settings.compress_job_save_kwargs + self.basic_job._compress_and_write_block( + read_blocks=read_blocks, + compressor=compressor, + max_windows_filename_len=max_windows_filename_len, + output_dir=output_dir, + output_format=output_format, + job_kwargs=job_kwargs, + ) + mock_bin_save.assert_has_calls( + [ + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment1_Record Node 101#NI-DAQmx-103" + ".PXIe-6341.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment1_Record Node 101#Neuropix-PXI-100" + ".ProbeB.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment1_Record Node 101#Neuropix-PXI-100" + ".ProbeC.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment3_Record Node 101#NI-DAQmx-103" + ".PXIe-6341.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment3_Record Node 101#Neuropix-PXI-100" + ".ProbeB.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment3_Record Node 101#Neuropix-PXI-100" + ".ProbeC.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment6_Record Node 101#NI-DAQmx-103" + ".PXIe-6341.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment6_Record Node 101#Neuropix-PXI-100" + ".ProbeB.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + call( + format="zarr", + folder=( + Path("output_dir") + / "compressed" + / ( + "experiment6_Record Node 101#Neuropix-PXI-100" + ".ProbeC.zarr" + ) + ), + compressor=WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + n_jobs=1, + ), + ], + any_order=True, + ) + + @patch("os.cpu_count") + @patch("warnings.warn") + @patch( + "spikeinterface.extractors.neoextractors.openephys" + ".OpenEphysBinaryRecordingExtractor.save" + ) + def test_compress_and_write_read_blocks_cpu_count( + self, + mock_bin_save: MagicMock, + _: MagicMock, + mock_os_cpu_count: MagicMock, + ): + """Tests _compress_and_write_block method with n_jobs set to -1""" + mock_os_cpu_count.return_value = 1 + read_blocks = self.basic_job._get_read_blocks() + compressor = self.basic_job._get_compressor() + max_windows_filename_len = ( + self.basic_job.job_settings.compress_max_windows_filename_len + ) + output_dir = ( + self.basic_job.job_settings.output_directory / "compressed" + ) + output_format = ( + self.basic_job.job_settings.compress_write_output_format + ) + self.basic_job._compress_and_write_block( + read_blocks=read_blocks, + compressor=compressor, + max_windows_filename_len=max_windows_filename_len, + output_dir=output_dir, + output_format=output_format, + job_kwargs={"n_jobs": -1}, + ) + self.assertEqual(9, len(mock_bin_save.mock_calls)) + + @patch("warnings.warn") + @patch( + "spikeinterface.extractors.neoextractors.openephys" + ".OpenEphysBinaryRecordingExtractor.save" + ) + @patch("platform.system") + def test_compress_and_write_windows_filename_error( + self, + mock_platform: MagicMock, + mock_bin_save: MagicMock, + _: MagicMock, + ): + """Tests _compress_and_write_block method when filename is too long + for Windows OS""" + mock_platform.return_value = "Windows" + read_blocks = self.basic_job._get_read_blocks() + compressor = self.basic_job._get_compressor() + max_windows_filename_len = 100 + output_dir = Path("x" * 100) + output_format = ( + self.basic_job.job_settings.compress_write_output_format + ) + job_kwargs = self.basic_job.job_settings.compress_job_save_kwargs + with self.assertRaises(Exception) as e: + self.basic_job._compress_and_write_block( + read_blocks=read_blocks, + compressor=compressor, + max_windows_filename_len=max_windows_filename_len, + output_dir=output_dir, + output_format=output_format, + job_kwargs=job_kwargs, + ) + self.assertEqual( + ( + "File name for zarr path is too long (156) and might lead " + "to errors. Use a shorter destination path.", + ), + e.exception.args, + ) + mock_bin_save.assert_not_called() + + @patch("warnings.warn") + @patch( + "aind_data_transformation.ephys.ephys_job.EphysCompressionJob" + "._compress_and_write_block" + ) + @patch( + "aind_data_transformation.ephys.ephys_job.EphysCompressionJob" + "._copy_and_clip_data" + ) + @patch("logging.info") + def test_compress_raw_data( + self, + mock_log_info: MagicMock, + mock_copy_and_clip_data: MagicMock, + mock_compress_and_write_block: MagicMock, + _: MagicMock, + ): + """Tests _compress_raw_data method with basic job""" + self.basic_job._compress_raw_data() + settings1_path = DATA_DIR / "Record Node 101" / "settings.xml" + settings3_path = DATA_DIR / "Record Node 101" / "settings_3.xml" + settings6_path = DATA_DIR / "Record Node 101" / "settings_6.xml" + mock_log_info.assert_has_calls( + [ + call(f"No NP-OPTO probes found in {settings1_path}"), + call(f"No NP-OPTO probes found in {settings3_path}"), + call(f"No NP-OPTO probes found in {settings6_path}"), + call("Clipping source data. This may take a minute."), + call("Finished clipping source data."), + call("Compressing source data."), + call("Finished compressing source data."), + ], + any_order=True, + ) + self.assertEqual(1, len(mock_copy_and_clip_data.mock_calls)) + # More granularity can be added in the future. For now, we just compare + # the length of the stream_gen list + actual_clip_args_derived = mock_copy_and_clip_data.mock_calls[0].kwargs + actual_clip_args_derived["stream_gen"] = len( + list(actual_clip_args_derived["stream_gen"]) + ) + expected_clip_args_derived = { + "stream_gen": 9, + "dst_dir": Path("output_dir") / "ecephys_clipped", + } + self.assertEqual(expected_clip_args_derived, actual_clip_args_derived) + + self.assertEqual(1, len(mock_compress_and_write_block.mock_calls)) + # More granularity can be added in the future. For now, we just compare + # the length of the read_blocks list + actual_comp_args_derived = mock_compress_and_write_block.mock_calls[ + 0 + ].kwargs + actual_comp_args_derived["read_blocks"] = len( + list(actual_comp_args_derived["read_blocks"]) + ) + expected_comp_args_derived = { + "read_blocks": 9, + "compressor": WavPack( + bps=0, + dynamic_noise_shaping=True, + level=3, + num_decoding_threads=8, + num_encoding_threads=1, + shaping_weight=0.0, + ), + "max_windows_filename_len": 150, + "output_dir": Path("output_dir") / "ecephys_compressed", + "output_format": "zarr", + "job_kwargs": {"n_jobs": 1}, + } + self.assertEqual(expected_comp_args_derived, actual_comp_args_derived) + + @patch("aind_data_transformation.ephys.ephys_job.datetime") + @patch( + "aind_data_transformation.ephys.ephys_job.EphysCompressionJob" + "._compress_raw_data" + ) + def test_run_job( + self, mock_compress_raw_data: MagicMock, mock_datetime: MagicMock + ): + """Tests run_job method""" + mock_start_time = datetime(2020, 10, 10, 1, 30, 0) + mock_end_time = datetime(2020, 10, 10, 5, 25, 17) + mock_time_delta = mock_end_time - mock_start_time + mock_datetime.now.side_effect = [ + datetime(2020, 10, 10, 1, 30, 0), + datetime(2020, 10, 10, 5, 25, 17), + ] + job_response = self.basic_job.run_job() + expected_job_response = JobResponse( + status_code=200, + message=f"Job finished in: {mock_time_delta}", + data=None, + ) + self.assertEqual(expected_job_response, job_response) + mock_compress_raw_data.assert_called_once() + + +class TestNpOptoCorrection(unittest.TestCase): + """Tests npopto_corrections module""" + + @classmethod + def setUpClass(cls): + """Read in the standard positions.""" + with open(NP_OPTO_CORRECT_DIR / "standard_positions.json", "r") as f: + standard_positions = json.load(f) + cls.standard_positions = standard_positions + + def test_get_standard_np_opto_electrode_positions(self): + """Tests get_standard_np_opto_electrode_positions class""" + output = get_standard_np_opto_electrode_positions() + self.assertEqual(self.standard_positions, list(output)) + + @patch("xml.etree.ElementTree.ElementTree.write") + @patch("pathlib.Path.rename") + @patch("logging.info") + def test_no_pxi_in_xml_file( + self, + mock_log_info: MagicMock, + mock_rename: MagicMock, + mock_write: MagicMock, + ): + """Tests correct_np_opto_electrode_locations method when no + Neuropix-PXI is found in xml file""" + correct_np_opto_electrode_locations( + input_dir=NP_OPTO_CORRECT_DIR / "settings_altered_no_pxi" + ) + mock_log_info.assert_not_called() + mock_rename.assert_not_called() + mock_write.assert_not_called() + + @patch("xml.etree.ElementTree.ElementTree.write") + @patch("pathlib.Path.rename") + @patch("logging.info") + def test_corrections_no_np_opto_probes_found( + self, + mock_log_info: MagicMock, + mock_rename: MagicMock, + mock_write: MagicMock, + ): + """Tests correct_np_opto_electrode_locations method when no np_opto + probes are found""" + settings_dir = NP_OPTO_CORRECT_DIR / "settings_2023_04" + correct_np_opto_electrode_locations(input_dir=settings_dir) + mock_log_info.assert_called_once_with( + f"No NP-OPTO probes found in {settings_dir / 'settings.xml'}" + ) + mock_rename.assert_not_called() + mock_write.assert_not_called() + + @patch("xml.etree.ElementTree.ElementTree.write") + @patch("pathlib.Path.rename") + @patch("logging.info") + def test_corrections_v_0_4_1( + self, + mock_log_info: MagicMock, + mock_rename: MagicMock, + mock_write: MagicMock, + ): + """Tests correct_np_opto_electrode_locations method when the + neuropixel version is 0.4.1""" + correct_np_opto_electrode_locations( + input_dir=NP_OPTO_CORRECT_DIR / "settings_2024_01" + ) + mock_log_info.assert_not_called() + mock_rename.assert_not_called() + mock_write.assert_not_called() + + @patch("xml.etree.ElementTree.ElementTree.write") + @patch("pathlib.Path.rename") + @patch("logging.info") + def test_needs_corrections( + self, + mock_log_info: MagicMock, + mock_rename: MagicMock, + mock_write: MagicMock, + ): + """Tests correct_np_opto_electrode_locations method when the + neuropixel version is 0.4.0""" + settings_dir = NP_OPTO_CORRECT_DIR / "settings_2022_07" + correct_np_opto_electrode_locations( + input_dir=NP_OPTO_CORRECT_DIR / "settings_2022_07" + ) + mock_log_info.assert_has_calls( + [ + call("Found NP-OPTO!"), + call( + f"Renaming wrong NP-OPTO settings file as " + f'{settings_dir / "settings.xml.wrong"}' + ), + call( + f"Saving correct NP-OPTO settings file as " + f'{settings_dir / "settings.xml"}' + ), + ] + ) + mock_rename.assert_called_once_with( + settings_dir / "settings.xml.wrong" + ) + mock_write.assert_called_once_with(str(settings_dir / "settings.xml")) + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/test_example.py b/tests/test_example.py deleted file mode 100644 index 06e9e0d..0000000 --- a/tests/test_example.py +++ /dev/null @@ -1,16 +0,0 @@ -"""Example test template.""" - -import unittest - - -class ExampleTest(unittest.TestCase): - """Example Test Class""" - - def test_assert_example(self): - """Example of how to test the truth of a statement.""" - - self.assertTrue(1 == 1) - - -if __name__ == "__main__": - unittest.main()