diff --git a/.github/workflows/tag_and_publish.yml b/.github/workflows/tag_and_publish.yml index ccc6605..9442a32 100644 --- a/.github/workflows/tag_and_publish.yml +++ b/.github/workflows/tag_and_publish.yml @@ -14,10 +14,10 @@ jobs: ref: ${{ env.DEFAULT_BRANCH }} fetch-depth: 0 token: ${{ secrets.SERVICE_TOKEN }} - - name: Set up Python 3.10 + - name: Set up Python 3.8 uses: actions/setup-python@v3 with: - python-version: '3.10' + python-version: '3.8' - name: Install dependencies run: | python -m pip install -e .[dev] --no-cache-dir @@ -64,55 +64,22 @@ jobs: secrets: SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }} publish: - runs-on: ubuntu-latest - env: - GO_VERSION: '1.14.12' - GO_OS: 'linux' - GO_ARCH: 'amd64' - SINGULARITY_VERSION: '3.7.0' needs: tag + runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 - name: Pull latest changes run: git pull origin main + - name: Set up Python 3.8 + uses: actions/setup-python@v2 + with: + python-version: 3.8 - name: Install dependencies run: | - sudo apt-get update && sudo apt-get install -y \ - build-essential \ - libssl-dev \ - uuid-dev \ - libgpgme11-dev \ - squashfs-tools \ - libseccomp-dev \ - wget \ - pkg-config \ - procps - - name: Install GO - run: | - wget https://dl.google.com/go/go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz - sudo tar -C /usr/local -xzvf go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz - sudo rm go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz - echo 'export PATH=$PATH:/usr/local/go/bin' | sudo tee -a /etc/profile - - name: Install Singularity - run: | - cd .. - wget https://github.com/hpcng/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz - sudo tar -xzf singularity-${SINGULARITY_VERSION}.tar.gz - sudo rm singularity-${SINGULARITY_VERSION}.tar.gz - echo "Finished installing binaries" - export PATH=$PATH:/usr/local/go/bin - cd singularity - sudo ./mconfig --without-suid - sudo make -C ./builddir - sudo make -C ./builddir install - - name: Build sif container - run: | - ls / - ls - mkdir build - sudo singularity build build/container.sif scripts/singularity_build.def - - name: Login and Deploy Container - run: | - echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ github.actor }} --password-stdin oras://ghcr.io - singularity push build/container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${{ needs.tag.outputs.new_version }} - singularity push build/container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:latest + 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 51a8319..e38bbc5 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: [ '3.9', '3.10', '3.11' ] + python-version: [ '3.8', '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 d6d7099..c82bd83 100644 --- a/README.md +++ b/README.md @@ -9,43 +9,41 @@ ## 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 - -Assuming `output_dir` exists: - -### From python +Please import this package and extend the abstract base class to define a new transformation job ```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) +from aind_data_transformation.core import ( + BasicJobSettings, + GenericEtl, + JobResponse, +) + +# An example JobSettings +class NewTransformJobSettings(BasicJobSettings): + # Add extra fields needed, for example, a random seed + random_seed: Optional[int] = 0 + +# An example EtlJob +class NewTransformJob(GenericEtl[NewTransformJobSettings]): + + # This method needs to be defined + def run_job(self) -> JobResponse: + """ + Main public method to run the transformation job + Returns + ------- + JobResponse + Information about the job that can be used for metadata downstream. + + """ + job_start_time = datetime.now() + # Do something here + job_end_time = datetime.now() + return JobResponse( + status_code=200, + message=f"Job finished in: {job_end_time-job_start_time}", + data=None, + ) -response = job.run_job() -``` - -### From the command line passing in settings as a json str -```bash -python -m aind_data_transformation.ephys.ephys_job --job-settings '{"input_source":"./tests/resources/v0.6.x_neuropixels_multiexp_multistream","output_directory":"output_dir"}' -``` - -### From the command line passing in settings via a config file -```bash -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 ``` diff --git a/pyproject.toml b/pyproject.toml index 1c23d00..d154432 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 = ">=3.9" +requires-python = ">=3.8" authors = [ {name = "Allen Institute for Neural Dynamics"} ] @@ -22,15 +22,7 @@ dependencies = [ ] [project.optional-dependencies] -ephys = [ - 'spikeinterface[full]>=0.100.5', - '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', @@ -48,7 +40,7 @@ version = {attr = "aind_data_transformation.__version__"} [tool.black] line-length = 79 -target_version = ['py39'] +target_version = ['py38'] exclude = ''' ( diff --git a/src/aind_data_transformation/ephys/__init__.py b/src/aind_data_transformation/ephys/__init__.py deleted file mode 100644 index c25a0ae..0000000 --- a/src/aind_data_transformation/ephys/__init__.py +++ /dev/null @@ -1 +0,0 @@ -"""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 deleted file mode 100644 index 40f92f5..0000000 --- a/src/aind_data_transformation/ephys/ephys_job.py +++ /dev/null @@ -1,453 +0,0 @@ -"""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." - ) - # compression for times is disabled - _ = rec.save( - format=output_format, - folder=zarr_path, - compressor=compressor, - compressor_by_dataset=dict(times=None), - **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 deleted file mode 100644 index 981d86d..0000000 --- a/src/aind_data_transformation/ephys/models.py +++ /dev/null @@ -1,25 +0,0 @@ -"""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 deleted file mode 100644 index ba2b4a5..0000000 --- a/src/aind_data_transformation/ephys/npopto_correction.py +++ /dev/null @@ -1,117 +0,0 @@ -"""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/np_opto_corrections/settings_2022_07/settings.xml b/tests/resources/np_opto_corrections/settings_2022_07/settings.xml deleted file mode 100644 index 2f33189..0000000 --- a/tests/resources/np_opto_corrections/settings_2022_07/settings.xml +++ /dev/null @@ -1,426 +0,0 @@ - - - - - 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 deleted file mode 100644 index 1d564d7..0000000 --- a/tests/resources/np_opto_corrections/settings_2023_04/settings.xml +++ /dev/null @@ -1,459 +0,0 @@ - - - - - 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 deleted file mode 100644 index 166ee58..0000000 --- a/tests/resources/np_opto_corrections/settings_2024_01/settings.xml +++ /dev/null @@ -1,676 +0,0 @@ - - - - - 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 deleted file mode 100644 index 23b2f17..0000000 --- a/tests/resources/np_opto_corrections/settings_altered_no_pxi/settings.xml +++ /dev/null @@ -1,703 +0,0 @@ - - - - - 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 deleted file mode 100644 index 00a1404..0000000 --- a/tests/resources/np_opto_corrections/standard_positions.json +++ /dev/null @@ -1,774 +0,0 @@ -[ - { - "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", - 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"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 deleted file mode 100644 index 9e0c6e2..0000000 --- a/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/experiment6/recording1/sync_messages.txt +++ /dev/null @@ -1,4 +0,0 @@ -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 deleted file mode 100644 index 51d287b..0000000 --- a/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings.xml +++ /dev/null @@ -1,752 +0,0 @@ - - - - - 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 deleted file mode 100644 index 2737d7b..0000000 --- a/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings_3.xml +++ /dev/null @@ -1,752 +0,0 @@ - - - - - 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 deleted file mode 100644 index 4ff8157..0000000 --- a/tests/resources/v0.6.x_neuropixels_multiexp_multistream/Record Node 101/settings_6.xml +++ /dev/null @@ -1,752 +0,0 @@ - - - - - 0.6.0 - 8 - 3 May 2022 11:25:28 - Windows 10 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - diff --git a/tests/test_ephys_job.py b/tests/test_ephys_job.py deleted file mode 100644 index 4d14c1a..0000000 --- a/tests/test_ephys_job.py +++ /dev/null @@ -1,1224 +0,0 @@ -"""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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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, - ), - compressor_by_dataset={"times": None}, - 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()