NWB Inspector

https://nwbinspector.readthedocs.io/en/dev/
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NWB Inspector is a Python-based package designed to assess the quality of Neurodata Without Borders...
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### Install NWBInspector using pip

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/installation.html

Use this command to install the NWBInspector package in a Python v3.10+ environment.

```bash
pip install nwbinspector

```

--------------------------------

### Install NWBInspector using Conda

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/installation.html

Install NWBInspector from the conda-forge release. This is recommended for MatNWB users.

```bash
conda install -c conda-forge nwbinspector

```

--------------------------------

### Install DANDI Streaming Dependencies

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_command_line_interface.html

Install additional dependencies required for streaming NWB files directly from the DANDI archive using `pip`.

```bash
pip install "nwbinspector[dandi]"
```

--------------------------------

### Example Check Implementation

Source: https://nwbinspector.readthedocs.io/en/dev/contributing_checks.html

Demonstrates a well-implemented check function for NWB files, ensuring experimenter information is present. This check is registered with specific importance and targets NWBFile neurodata types.

```python
import typing as tp

from pynwb.file import NWBFile

from ..inspector import InspectorMessage, Importance
from ..utils import register_check


@register_check(
    importance=Importance.BEST_PRACTICE_SUGGESTION,
    neurodata_type=NWBFile
)
def check_experimenter(nwbfile: NWBFile) -> tp.Optional[InspectorMessage]:
    """Check if an experimenter has been added for the session."""
    if not nwbfile.experimenter:
        return InspectorMessage(
            message="Experimenter is missing. Add experimenter information to improve metadata completeness."
        )
    return None

```

--------------------------------

### Unit Tests for a New NWBInspector Check

Source: https://nwbinspector.readthedocs.io/en/dev/contributing_checks.html

Example unit tests for a new check, demonstrating how to test both passing and failing scenarios. The `assert` statements verify that the check returns `None` for valid inputs and an `InspectorMessage` for invalid inputs.

```python
from src.nwbinspector.checks._my_feature import check_my_feature
from src.nwbinspector.testing import make_minimal_nwbfile
from nwbinspector.core import InspectorMessage

def test_my_feature_pass():
    # Test case where check should pass
    assert check_my_feature(nwbfile=NWBFile(...)) is None

def test_my_feature_fail():
    # Test case where check should fail
    assert check_my_feature(nwbfile=make_minimal_nwbfile()) == InspectorMessage(
        message="Expected message"
    )

```

--------------------------------

### is_module_installed()

Source: https://nwbinspector.readthedocs.io/en/dev/api/utils.html

Checks if a given module is installed on the system.

```APIDOC
## is_module_installed()

### Description
Check if the given module is installed on the system. Used for lazy imports.

### Method
N/A (Function)

### Parameters

#### Input Parameters

- **module_name** (str) - The name of the module to check.

### Returns
- bool: True if the module is installed, False otherwise.
```

--------------------------------

### Linking Check to Best Practice Documentation (Standard)

Source: https://nwbinspector.readthedocs.io/en/dev/contributing_checks.html

This example shows how to link a check function to its corresponding best practice documentation using a standard reStructuredText format. The `:py:meth:` directive is used to create a link to the check function's API documentation.

```rst
.. _best_practice_my_feature:

My Feature
~~~~~~~~~~

Description of the best practice.

Check function: :py:meth:`~nwbinspector.checks._tables.check_my_feature`

```

--------------------------------

### Template for a New NWBInspector Check

Source: https://nwbinspector.readthedocs.io/en/dev/contributing_checks.html

This is a template for creating a new check function. It includes the necessary decorator, type hints, and return structure for a valid check. Ensure the function name starts with 'check_' and the message is clear and actionable.

```python
import { Importance, InspectorMessage, register_check } from "@nwbinspector/core"
import { NWBFile } from "@nwbinspector/types"
import { Optional } from "@nwbinspector/utils"

@register_check(
    importance=Importance.BEST_PRACTICE_SUGGESTION,  # Choose appropriate level
    neurodata_type=NWBFile  # Most general applicable type
)
def check_my_feature(nwbfile: NWBFile) -> Optional[InspectorMessage]:
    """One-line description of what this check validates."""
    if problem_detected:
        return InspectorMessage(
            message="Clear description of the issue and how to fix it."
        )
    return None

```

--------------------------------

### Linking Check to Best Practice Documentation (Custom Ref)

Source: https://nwbinspector.readthedocs.io/en/dev/contributing_checks.html

This example demonstrates how to link a check function to a specific best practice section using a custom reference label within the docstring. This is useful when the best practice section label does not automatically match the check function name.

```python
def check_my_feature(nwbfile: NWBFile) -> Optional[InspectorMessage]:
    """
    One-line description of what this check validates.

    Best Practice: :ref:`best_practice_my_feature_unique_label`
    """

```

--------------------------------

### View All CLI Options

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_command_line_interface.html

Call the `nwbinspector --help` command to view all available options and arguments for the CLI.

```bash
nwbinspector --help
```

--------------------------------

### Loading Configuration

Source: https://nwbinspector.readthedocs.io/en/dev/api/tools.html

Use `load_config` to load configuration settings, either from a specified file path or by using internal keywords like 'dandi'.

```python
load_config(_filepath_or_keyword : str | Path_) → dict
    
Load a config dictionary either via keyword search of the internal configs, or an explicit filepath.
```

--------------------------------

### check_time_intervals_stop_after_start

Source: https://nwbinspector.readthedocs.io/en/dev/api/checks.html

Checks that all stop times on a TimeInterval object occur after their corresponding start times. This is crucial for valid time interval data.

```APIDOC
## check_time_intervals_stop_after_start

### Description
Check that all stop times on a TimeInterval object occur after their corresponding start times.
Best Practice: Timing Columns

### Method
N/A (Function Call)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
* **_time_intervals** (TimeIntervals_) - The TimeIntervals object to check.
* **_nelems** (int | None, optional) - Only check the first {nelems} elements. This is useful in case there columns are very long so you don’t need to load the entire array into memory. Use None to load the entire arrays. Defaults to 200.
```

--------------------------------

### get_nwbfiles_from_path

Source: https://nwbinspector.readthedocs.io/en/dev/api/utils.html

Given a path, return a list of NWB files. A directory whose name ends with `.nwb.zarr` is treated as a single NWB file (a Zarr store), not as a folder to recurse into. Other directories are recursed for `*.nwb*` paths.

```APIDOC
## get_nwbfiles_from_path

### Description
Given a path, return a list of NWB files. A directory whose name ends with `.nwb.zarr` is treated as a single NWB file (a Zarr store), not as a folder to recurse into. Other directories are recursed for `*.nwb*` paths.

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Method
N/A (Python function)

### Endpoint
N/A (Python function)

### Parameters
* **path** (_PathType_) – Path to search for NWB files.

### Response
#### Success Response
**list[Path]** – A list of paths to NWB files.

Return type:
    
list[Path]
```

--------------------------------

### ImageSeries Checks

Source: https://nwbinspector.readthedocs.io/en/dev/api/register_check.html

Functions for validating ImageSeries data, including external file validity, relative paths, data size, and starting frames.

```APIDOC
## ImageSeries Checks

### Description
Functions for validating ImageSeries data, including external file validity, relative paths, data size, and starting frames.

### Functions
- `check_image_series_external_file_valid()`
- `check_image_series_external_file_relative()`
- `check_image_series_data_size()`
- `check_image_series_starting_frame_without_external_file()
```

--------------------------------

### Custom JSONEncoder for NWBInspector

Source: https://nwbinspector.readthedocs.io/en/dev/api/tools.html

Subclass JSONEncoder to handle objects that cannot be serialized by default. This example shows how to support arbitrary iterators by converting them to lists.

```python
def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return super().default(o)

```

--------------------------------

### check_time_series_duration

Source: https://nwbinspector.readthedocs.io/en/dev/api/checks.html

Checks if the duration of a TimeSeries exceeds a specified threshold, calculated from timestamps or start time, rate, and data length. Defaults to 1 year.

```APIDOC
## check_time_series_duration

### Description
Check if the TimeSeries duration is longer than the specified threshold. The default threshold is 1 year (31,557,600 seconds = 365.25 days). Duration is calculated from either timestamps or starting_time + rate + data length.
Best Practice: Units of Measurement

### Method
N/A (Function Call)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
*   **_time_series** (TimeSeries_) - Required - The TimeSeries object to check.
*   **_duration_threshold** (float) - Optional - Defaults to 31557600.0. The duration threshold in seconds.

### Response
#### Success Response
- **InspectorMessage | None** - Returns an InspectorMessage if the duration exceeds the threshold, otherwise None.
```

--------------------------------

### Create and Push Git Tag for Release

Source: https://nwbinspector.readthedocs.io/en/dev/developer_guide.html

Create a signed Git tag for a new release and push it to GitHub. This is a step in the release process to mark a specific version.

```bash
release=X.Y.Z
git tag ${release} --sign -m "nwbinspector ${release}"
git push --tags
```

--------------------------------

### Object Reference Data Type for Links

Source: https://nwbinspector.readthedocs.io/en/dev/best_practices/extensions.html

Use a dataset with an object reference data type to store collections of links to other objects. This example shows a dtype for a dataset of links to TimeSeries.

```yaml
dtype:
    target_type: TimeSeries
    reftype: object
```

--------------------------------

### inspect_all

Source: https://nwbinspector.readthedocs.io/en/dev/api/utils.html

Inspects a local NWBFile or a folder of NWBFiles and returns suggestions for improvements according to best practices. It can recursively scan all NWBFiles present in a directory.

```APIDOC
## inspect_all

### Description
Inspect a local NWBFile or folder of NWBFiles and return suggestions for improvements according to best practices.

### Method
N/A (Function Signature)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
* **path** (_PathType_) – File path to an NWBFile, folder path to iterate over recursively and scan all NWBFiles present, or a six-digit identifier of the DANDISet.
* **config** (_dict, optional_) – If a dictionary, it must be valid against our JSON configuration schema. Can specify a mapping of importance levels and list of check functions whose importance you wish to change. Typically loaded via json.load from a valid .json file
* **ignore** (_list of strings, optional_) – Names of functions to skip.
* **select** (_list of strings, optional_) – Names of functions to pick out of available checks.
* **importance_threshold** (_string or Importance, optional_) – Ignores tests with an assigned importance below this threshold. Importance has three levels: CRITICAL, BEST_PRACTICE_VIOLATION, BEST_PRACTICE_SUGGESTION. The default is the lowest level, BEST_PRACTICE_SUGGESTION.
* **n_jobs** (_int_) – Number of jobs to use in parallel. Set to -1 to use all available resources. This may also be a negative integer x from -2 to -(number_of_cpus - 1) which acts like negative slicing by using all available CPUs minus x. Set to 1 (also the default) to disable.
* **skip_validate** (_bool, optional_) – Skip the PyNWB validation step. The default is False, which is recommended.
* **progress_bar** (_bool, optional_) – Display a progress bar while scanning NWBFiles. Defaults to True.
* **progress_bar_class** (_type of tqdm.tqdm, optional_) – The specific child class of tqdm.tqdm to use to make progress bars. Defaults to tqdm.tqdm, the most generic parent.
* **progress_bar_options** (_dict, optional_) – Dictionary of keyword arguments to pass directly to the progress_bar_class.
* **modules** (_list of strings, optional_) – List of external module names to load; examples would be namespace extensions. These modules may also contain their own custom checks for their extensions.

### Returns
Iterable[InspectorMessage | None]
```

--------------------------------

### Inspect a Dandiset by ID

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_library.html

Use `inspect_dandiset` to stream and inspect data directly from the DANDI Archive using its ID. This is efficient for large datasets that are impractical to download fully. Ensure `nwbinspector[dandi]` is installed.

```python
from nwbinspector import inspect_dandiset

dandiset_id = "000004"

messages = list(inspect_dandiset(dandiset_id=dandiset_id))

```

```python
from nwbinspector import inspect_dandiset

dandiset_id = "000004"
dandiset_version = "0.220126.1851"

messages = list(inspect_dandiset(dandiset_id=dandiset_id, dandiset_version=dandiset_version))

```

--------------------------------

### inspect_all

Source: https://nwbinspector.readthedocs.io/en/dev/api/nwbinspector.html

Inspects a local NWBFile or folder of NWBFiles and returns suggestions for improvements according to best practices. It can process multiple files in parallel and offers various configuration options.

```APIDOC
## inspect_all

### Description
Inspect a local NWBFile or folder of NWBFiles and return suggestions for improvements according to best practices.

### Method
inspect_all

### Parameters
#### Path Parameters
* **path** (PathType) - Required - File path to an NWBFile, folder path to iterate over recursively and scan all NWBFiles present, or a six-digit identifier of the DANDISet.

#### Optional Parameters
* **config** (dict | None) - If a dictionary, it must be valid against our JSON configuration schema. Can specify a mapping of importance levels and list of check functions whose importance you wish to change. Typically loaded via json.load from a valid .json file.
* **ignore** (list[str] | None) - Names of functions to skip.
* **select** (list[str] | None) - Names of functions to pick out of available checks.
* **importance_threshold** (str | Importance) - Ignores tests with an assigned importance below this threshold. Importance has three levels: CRITICAL (potentially incorrect data), BEST_PRACTICE_VIOLATION (very suboptimal data representation), BEST_PRACTICE_SUGGESTION (improvable data representation). The default is the lowest level, BEST_PRACTICE_SUGGESTION.
* **n_jobs** (int) - Number of jobs to use in parallel. Set to -1 to use all available resources. This may also be a negative integer x from -2 to -(number_of_cpus - 1) which acts like negative slicing by using all available CPUs minus x. Set to 1 (also the default) to disable.
* **skip_validate** (bool) - Skip the PyNWB validation step. The default is False, which is recommended.
* **progress_bar** (bool) - Display a progress bar while scanning NWBFiles. Defaults to True.
* **progress_bar_class** (Type[tqdm]) - The specific child class of tqdm.tqdm to use to make progress bars. Defaults to tqdm.tqdm, the most generic parent.
* **progress_bar_options** (dict | None) - Dictionary of keyword arguments to pass directly to the progress_bar_class.
* **stream** (bool) - Stream results.
* **version_id** (str | None) - Version identifier.
* **modules** (list[str] | None) - List of external module names to load; examples would be namespace extensions. These modules may also contain their own custom checks for their extensions.

### Returns
Iterable[InspectorMessage | None]
```

--------------------------------

### Load External Modules with NWBI

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_command_line_interface.html

Use the `--modules` flag to load external check registries. Provide module names exactly as they are imported in Python, comma-separated without spaces if multiple.

```bash
nwbinspector path/to/my/data.nwb --modules my_extension_module1,my_extension_module2

```

--------------------------------

### Define New Neurodata Type with CamelCase

Source: https://nwbinspector.readthedocs.io/en/dev/best_practices/extensions.html

When defining a new neurodata type using `neurodata_type_def`, use camelCase notation. Names should not include spaces, must start with an uppercase letter, and use a single capitalized letter to separate parts of the name.

```python
neurodata_type_def: LaserMeasurement
```

--------------------------------

### load_config Function

Source: https://nwbinspector.readthedocs.io/en/dev/api/tools.html

Loads a configuration dictionary either via keyword search or an explicit filepath.

```APIDOC
## load_config

### Description
Load a config dictionary either via keyword search of the internal configs, or an explicit filepath.

### Parameters
- **filepath_or_keyword** (str | Path) - Required - Either a file path to the configuration file or a keyword (e.g., 'dandi') to load predefined configurations.
```

--------------------------------

### Inspect a Single NWB File

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_command_line_interface.html

Supply a path to a single NWB file to perform a basic inspection and display a report to the console.

```bash
nwbinspector path/to/my/data.nwb
```

--------------------------------

### _get_report_header

Source: https://nwbinspector.readthedocs.io/en/dev/api/tools.html

Grabs basic system information at the time of report generation.

```APIDOC
## _get_report_header

### Description
Grab basic information from system at time of report generation.

### Method
N/A (Python function)

### Parameters
None

### Returns
* **dict[str, str]** - A dictionary containing basic system information.
```

--------------------------------

### Run Checks on NWBFile

Source: https://nwbinspector.readthedocs.io/en/dev/api/tools.html

Executes a list of check functions on an NWBFile object. Supports optional progress bar customization.

```python
run_checks(_nwbfile : NWBFile_, _checks : list_, _progress_bar_class : Type[tqdm] | None = None_, _progress_bar_options : dict | None = None_, _nwb_schema_version : Version | None = None_) → Iterable[InspectorMessage | None]
```

--------------------------------

### Inspect All NWB Files in a Directory or List

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_library.html

Use `inspect_all` to replicate the command-line interface behavior by inspecting all NWB files within a specified directory or a list of file paths. The return structure is identical to `inspect_nwbfile`.

```python
from nwbinspector import inspect_all

all_results = list(inspect_all(path=file_paths_or_folder, ...))

```

--------------------------------

### Inspect an NWB Directory

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_command_line_interface.html

Supply a path to a directory containing NWB files. The tool will recursively inspect all NWB files within the directory and its subdirectories.

```bash
nwbinspector path/to/my/data/dir/
```

--------------------------------

### inspect_nwbfile

Source: https://nwbinspector.readthedocs.io/en/dev/api/nwbinspector.html

Opens an NWB file, inspects its contents, and returns suggestions for improvements according to best practices. This function is suitable for inspecting individual NWB files.

```APIDOC
## inspect_nwbfile

### Description
Open an NWB file, inspect the contents, and return suggestions for improvements according to best practices.

### Method
inspect_nwbfile

### Parameters
#### Path Parameters
* **nwbfile_path** (FilePathType) - Required - Path to the NWB file on disk or on S3.

#### Optional Parameters
* **driver** (str | None) - Driver to use for opening the file.
* **skip_validate** (bool) - Skip the PyNWB validation step. The default is False, which is recommended.
* **max_retries** (int | None) - Maximum number of retries for opening the file.
* **checks** (list | None) - List of checks to run.
* **config** (dict) - Dictionary valid against our JSON configuration schema. Can specify a mapping of importance levels and list of check functions whose importance you wish to change. Typically loaded via json.load from a valid .json file.
* **ignore** (list | None) - Names of functions to skip.
* **select** (list | None) - Names of functions to pick out of available checks.
* **importance_threshold** (str | Importance) - Ignores tests with an assigned importance below this threshold. Importance has three levels: CRITICAL (potentially incorrect data), BEST_PRACTICE_VIOLATION (very suboptimal data representation), BEST_PRACTICE_SUGGESTION (improvable data representation). The default is the lowest level, BEST_PRACTICE_SUGGESTION.

### Returns
Iterable[InspectorMessage | None]
```

--------------------------------

### inspect_nwbfile_object

Source: https://nwbinspector.readthedocs.io/en/dev/api/utils.html

Inspects an in-memory NWBFile object and returns suggestions for improvements based on best practices.

```APIDOC
## inspect_nwbfile_object

### Description
Inspect an in-memory NWBFile object and return suggestions for improvements according to best practices.

### Method
Not applicable (Python function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
* **nwbfile_object** (_NWBFile_) – An in-memory NWBFile object.
* **checks** (_list, optional_) – list of checks to run
* **config** (_dict, optional_) – Dictionary valid against our JSON configuration schema. Can specify a mapping of importance levels and list of check functions whose importance you wish to change. Typically loaded via json.load from a valid .json file
* **ignore** (_list, optional_) – Names of functions to skip.
* **select** (_list, optional_) – Names of functions to pick out of available checks.
* **importance_threshold** (_string or Importance, optional_) – Ignores tests with an assigned importance below this threshold. Importance has three levels:
    * CRITICAL: potentially incorrect data
    * BEST_PRACTICE_VIOLATION: very suboptimal data representation
    * BEST_PRACTICE_SUGGESTION: improvable data representation
The default is the lowest level, BEST_PRACTICE_SUGGESTION.

### Response
#### Success Response
Yields: **results** (_a generator of InspectorMessage objects_) – A generator that returns a message on each iteration, if any are triggered by downstream conditions. Otherwise, has length zero (if cast as list), or raises StopIteration (if explicitly calling next).

#### Response Example
None provided.
```

--------------------------------

### Apply DANDI Configuration for Inspection

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_library.html

Load the DANDI configuration using `load_config("dandi")` to adjust check importance levels for DANDI Archive compliance. Apply this configuration to inspection functions like `inspect_nwbfile`.

```python
from nwbinspector import inspect_nwbfile, load_config

dandi_config = load_config("dandi")
results = list(inspect_nwbfile(nwbfile_path="path_to_single_nwbfile", config=dandi_config))

```

--------------------------------

### General NWB File Checks

Source: https://nwbinspector.readthedocs.io/en/dev/api/register_check.html

General utility functions for checking common naming conventions and descriptions within NWB files.

```APIDOC
## General NWB File Checks

### Description
General utility functions for checking common naming conventions and descriptions within NWB files.

### Functions
- `check_name_slashes()`
- `check_name_colons()`
- `check_description()
```

--------------------------------

### check_small_dataset_compression

Source: https://nwbinspector.readthedocs.io/en/dev/api/checks.html

Checks if h5py Datasets within an NWBContainer have compression enabled. A warning is issued if the dataset size falls within a specified range and lacks compression.

```APIDOC
## check_small_dataset_compression

### Description
Checks if h5py Datasets within an NWBContainer have compression enabled. A warning is issued if the dataset size falls within a specified range and lacks compression.

### Method
None (Function Call)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
* **_nwb_container** (NWBContainer) - The NWBContainer to check.
* **_gb_severity_threshold** (float, optional) - A severity threshold in GB. Defaults to 10.0.
* **_mb_lower_bound** (float, optional) - The lower bound in MB for a dataset to be checked. Defaults to 50.0.
* **_gb_upper_bound** (float, optional) - The upper bound in GB for a dataset to be checked. Defaults to 20.0.

### Response
* **InspectorMessage | None** - Returns an InspectorMessage if compression is not enabled for a dataset within the specified bounds, otherwise None.
```

--------------------------------

### Stream Inspect NWB Data from DANDI Archive

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_command_line_interface.html

Specify the DANDI set ID as the path and use the `--stream` flag to inspect NWB files directly from the DANDI archive without downloading. The default configuration becomes 'dandi' when streaming.

```bash
nwbinspector 000017 --stream
```

--------------------------------

### inspect_nwbfile_object

Source: https://nwbinspector.readthedocs.io/en/dev/api/nwbinspector.html

Inspects an in-memory NWBFile object and returns suggestions for improvements based on best practices. Allows for customization of checks, configuration, and importance thresholds.

```APIDOC
## inspect_nwbfile_object

### Description
Inspect an in-memory NWBFile object and return suggestions for improvements according to best practices.

### Method
N/A (Function Call)

### Parameters
#### Function Parameters
- **nwbfile_object** (NWBFile) - Required - An in-memory NWBFile object.
- **checks** (list | None) - Optional - list of checks to run
- **config** (dict | None) - Optional - Dictionary valid against our JSON configuration schema. Can specify a mapping of importance levels and list of check functions whose importance you wish to change. Typically loaded via json.load from a valid .json file
- **ignore** (list[str] | None) - Optional - Names of functions to skip.
- **select** (list[str] | None) - Optional - Names of functions to pick out of available checks.
- **importance_threshold** (str | Importance) - Optional - Ignores tests with an assigned importance below this threshold. Importance has three levels: CRITICAL (* potentially incorrect data), BEST_PRACTICE_VIOLATION (* very suboptimal data representation), BEST_PRACTICE_SUGGESTION (* improvable data representation). The default is the lowest level, BEST_PRACTICE_SUGGESTION.

### Returns
Iterable[InspectorMessage | None] - An iterable of InspectorMessage objects or None.
```

--------------------------------

### Parallel Inspection with N-Jobs

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_command_line_interface.html

Use the `--n-jobs` flag to enable parallel processing over a directory. Set to a positive integer for specific CPU count or -1 to use all available resources.

```bash
nwbinspector path/to/my/data/dir/ --n-jobs -1

```

--------------------------------

### Format Report by Levels

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_command_line_interface.html

Organize the report output by specifying a comma-separated list of attributes from InspectorMessage. The order of levels can be customized.

```bash
nwbinspector path/to/my/data/dir/ --levels check_function_name,object_type,file_path
```

--------------------------------

### run_checks

Source: https://nwbinspector.readthedocs.io/en/dev/api/utils.html

Runs checks on an open NWBFile object.

```APIDOC
## run_checks

### Description
Run checks on an open NWBFile object.

### Method
Not applicable (Python function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
* **nwbfile** (_pynwb.NWBFile_) – The in-memory pynwb.NWBFile object to run the checks on.
* **checks** (_list of check functions_) – The list of check functions that will be run on the in-memory pynwb.NWBFile object.
* **progress_bar_class** (_type of tqdm.tqdm, optional_) – The specific child class of tqdm.tqdm to use to make progress bars. Defaults to not displaying progress per set of checks over an individual file.
* **progress_bar_options** (_dict, optional_) – Dictionary of keyword arguments to pass directly to the progress_bar_class.
* **nwb_schema_version** (_packaging.version.Version, optional_) – The NWB schema version of the file being inspected. If not provided, will be read from nwbfile.read_io.nwb_version if available. This arg is mostly used for tests. Usually it is best to leave as None.

### Response
#### Success Response
Yields: **results** (_a generator of InspectorMessage objects_) – A generator that returns a message on each iteration, if any are triggered by downstream conditions. Otherwise, has length zero (if cast as list), or raises StopIteration (if explicitly calling next).

#### Response Example
None provided.
```

--------------------------------

### General NWB Checks

Source: https://nwbinspector.readthedocs.io/en/dev/index.html

General utility functions for checking common naming conventions and descriptions within NWB files.

```APIDOC
## General NWB Checks

### Description
General utility functions for checking common naming conventions and descriptions within NWB files.

### Functions
- `check_name_slashes()`
- `check_name_colons()`
- `check_description()
```

--------------------------------

### Select Specific Checks

Source: https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_command_line_interface.html

Use the `--select` flag to specify a comma-separated list of checks to run. This is useful when you only want to execute a subset of available checks.

```bash
nwbinspector path/to/my/data.nwb --select check_subject_exists,check_subject_species_exists

```

--------------------------------

### NWB Container Checks

Source: https://nwbinspector.readthedocs.io/en/dev/api/nwbinspector.html

Functions to check compression settings for datasets within NWB containers.

```APIDOC
## NWB Container Checks

### Description
Checks related to compression settings for datasets within NWB containers.

### Functions
- `check_large_dataset_compression()`
- `check_small_dataset_compression()`
- `check_empty_string_for_optional_attribute()`
```

--------------------------------

### General Checks

Source: https://nwbinspector.readthedocs.io/en/dev/api/utils.html

General utility functions for checking string formats and descriptions.

```APIDOC
## Check Functions: General

### Description
General utility functions for validating common data formats.

### Functions
- `check_name_slashes()`
- `check_name_colons()`
- `check_description()
```

--------------------------------

### check_large_dataset_compression

Source: https://nwbinspector.readthedocs.io/en/dev/api/checks.html

Checks if large h5py Datasets within an NWBContainer have compression enabled. A warning is issued if the dataset size exceeds a specified bound.

```APIDOC
## check_large_dataset_compression

### Description
Checks if large h5py Datasets within an NWBContainer have compression enabled. A warning is issued if the dataset size exceeds a specified bound.

### Method
None (Function Call)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
* **_nwb_container** (NWBContainer) - The NWBContainer to check.
* **_gb_lower_bound** (float, optional) - The lower bound in GB for a dataset to be considered 'large'. Defaults to 20.0.

### Response
* **InspectorMessage | None** - Returns an InspectorMessage if compression is not enabled for a large dataset, otherwise None.
```

--------------------------------

### calculate_number_of_cpu()

Source: https://nwbinspector.readthedocs.io/en/dev/api/utils.html

Calculates the number of CPUs to use, considering requested and available resources.

```APIDOC
## calculate_number_of_cpu()

### Description
Calculate the number CPUs to use with respect to negative slicing and check against maximal available resources.

### Method
N/A (Function)

### Parameters

#### Input Parameters

- **requested_cpu** (int, optional) - The desired number of CPUs to use. The default is 1.

### Returns
- int: The calculated number of CPUs to use.
```

--------------------------------

### print_to_console

Source: https://nwbinspector.readthedocs.io/en/dev/api/tools.html

Prints a list of formatted messages to the console.

```APIDOC
## print_to_console

### Description
Print report file contents to console.

### Parameters
* **_formatted_messages** (_list[str]_) –

### Returns
None
```

--------------------------------

### get_package_version()

Source: https://nwbinspector.readthedocs.io/en/dev/api/utils.html

Retrieves the version of a package.

```APIDOC
## get_package_version()

### Description
Retrieve the version of a package regardless of if it has a __version__ attribute set.

### Method
N/A (Function)

### Parameters

#### Input Parameters

- **name** (str) - Name of package.

### Returns
- Version: The package version as an object from packaging.version.Version, which allows comparison to other versions.
```

--------------------------------

### run_checks

Source: https://nwbinspector.readthedocs.io/en/dev/api/nwbinspector.html

Runs a specified list of checks on an open NWBFile object. Supports progress bar customization for monitoring check execution.

```APIDOC
## run_checks

### Description
Run checks on an open NWBFile object.

### Method
N/A (Function Call)

### Parameters
#### Function Parameters
- **nwbfile** (NWBFile) - Required - The in-memory pynwb.NWBFile object to run the checks on.
- **checks** (list) - Required - The list of check functions that will be run on the in-memory pynwb.NWBFile object.
- **progress_bar_class** (Type[tqdm] | None) - Optional - The specific child class of tqdm.tqdm to use to make progress bars. Defaults to not displaying progress per set of checks over an individual file.
- **progress_bar_options** (dict | None) - Optional - Dictionary of keyword arguments to pass directly to the progress_bar_class.
- **nwb_schema_version** (Version | None) - Optional - The NWB schema version of the file being inspected. If not provided, will be read from nwbfile.read_io.nwb_version if available. This arg is mostly used for tests. Usually it is best to leave as None.

### Yields
Iterable[InspectorMessage | None] - A generator that returns a message on each iteration, if any are triggered by downstream conditions. Otherwise, has length zero (if cast as list), or raises StopIteration (if explicitly calling next).
```

--------------------------------

### Core Functions

Source: https://nwbinspector.readthedocs.io/en/dev/api/tools.html

Core functions for inspecting NWB files, DANDI datasets, and remote URLs.

```APIDOC
## Core Functions

### Description
Core functions for inspecting NWB files and related data structures.

### Functions
- `inspect_all()`
- `_pickle_inspect_nwb()`
- `inspect_nwbfile()`
- `_intercept_in_vitro_protein()`
- `inspect_nwbfile_object()`
- `run_checks()`
- `inspect_dandiset()`
- `inspect_dandi_file_path()`
- `inspect_url()
```

--------------------------------

### NWB Containers Checks

Source: https://nwbinspector.readthedocs.io/en/dev/api/tools.html

Functions to check compression settings for datasets within NWB containers.

```APIDOC
## Check Functions: NWB Containers

### Description
Functions for checking compression settings on NWB container datasets.

### Functions
- `check_large_dataset_compression()`
- `check_small_dataset_compression()`
- `check_empty_string_for_optional_attribute()
```
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