Add high level APIs #80
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
WalkthroughThe latest update to the Changes
Recent Review DetailsConfiguration used: CodeRabbit UI Files selected for processing (2)
Files skipped from review as they are similar to previous changes (1)
Additional comments not posted (1)
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (invoked as PR comments)
Additionally, you can add CodeRabbit Configration File (
|
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #80 +/- ##
==========================================
+ Coverage 94.79% 95.16% +0.37%
==========================================
Files 13 13
Lines 1498 1551 +53
==========================================
+ Hits 1420 1476 +56
+ Misses 78 75 -3 ☔ View full report in Codecov by Sentry. |
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 1
Actionable comments outside the diff hunks (1)
sleap_io/model/video.py (1)
Line range hint
97-97: Avoid using a bareexceptstatement. It's better to specify the exceptions you expect to handle to avoid masking other unexpected issues.- except: + except ExpectedExceptionType:
Comment on lines
24
to
29
| save_labelstudio, | ||
| load_jabs, | ||
| save_jabs, | ||
| load_video, | ||
| load_file, | ||
| ) |
There was a problem hiding this comment.
📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [7-28]
Several imports in this file are marked as unused. If these are not intended for external use, consider adding them to the __all__ list to explicitly define what is exported by this module, or remove them if they are not needed.
- from sleap_io.model.skeleton import Node, Edge, Skeleton, Symmetry
- from sleap_io.model.video import Video
- from sleap_io.model.instance import (
- Point,
- PredictedPoint,
- Track,
- Instance,
- PredictedInstance,
- )
- from sleap_io.model.labeled_frame import LabeledFrame
- from sleap_io.model.labels import Labels
- from sleap_io.io.main import (
- load_slp,
- save_slp,
- load_nwb,
- save_nwb,
- load_labelstudio,
- save_labelstudio,
- load_jabs,
- save_jabs,
- )
Comment on lines
+128
to
+209
| def load_file( | ||
| filename: str | Path, format: Optional[str] = None, **kwargs | ||
| ) -> Union[Labels, Video]: | ||
| """Load a file and return the appropriate object. | ||
|
|
||
| Args: | ||
| filename: Path to a file. | ||
| format: Optional format to load as. If not provided, will be inferred from the | ||
| file extension. Available formats are: "slp", "nwb", "labelstudio", "jabs" | ||
| and "video". | ||
|
|
||
| Returns: | ||
| A `Labels` or `Video` object. | ||
| """ | ||
| if isinstance(filename, Path): | ||
| filename = str(filename) | ||
|
|
||
| if format is None: | ||
| if filename.endswith(".slp"): | ||
| format = "slp" | ||
| elif filename.endswith(".nwb"): | ||
| format = "nwb" | ||
| elif filename.endswith(".json"): | ||
| format = "json" | ||
| elif filename.endswith(".h5"): | ||
| format = "jabs" | ||
| else: | ||
| for vid_ext in Video.EXTS: | ||
| if filename.endswith(vid_ext): | ||
| format = "video" | ||
| break | ||
| if format is None: | ||
| raise ValueError(f"Could not infer format from filename: '{filename}'.") | ||
|
|
||
| if filename.endswith(".slp"): | ||
| return load_slp(filename, **kwargs) | ||
| elif filename.endswith(".nwb"): | ||
| return load_nwb(filename, **kwargs) | ||
| elif filename.endswith(".json"): | ||
| return load_labelstudio(filename, **kwargs) | ||
| elif filename.endswith(".h5"): | ||
| return load_jabs(filename, **kwargs) | ||
| elif format == "video": | ||
| return load_video(filename, **kwargs) | ||
|
|
||
|
|
||
| def save_file( | ||
| labels: Labels, filename: str | Path, format: Optional[str] = None, **kwargs | ||
| ): | ||
| """Save a file based on the extension. | ||
|
|
||
| Args: | ||
| labels: A SLEAP `Labels` object (see `load_slp`). | ||
| filename: Path to save labels to. | ||
| format: Optional format to save as. If not provided, will be inferred from the | ||
| file extension. Available formats are: "slp", "nwb", "labelstudio" and | ||
| "jabs". | ||
| """ | ||
| if isinstance(filename, Path): | ||
| filename = str(filename) | ||
|
|
||
| if format is None: | ||
| if filename.endswith(".slp"): | ||
| format = "slp" | ||
| elif filename.endswith(".nwb"): | ||
| format = "nwb" | ||
| elif filename.endswith(".json"): | ||
| format = "labelstudio" | ||
| elif "pose_version" in kwargs: | ||
| format = "jabs" | ||
|
|
||
| if format == "slp": | ||
| save_slp(labels, filename, **kwargs) | ||
| elif format == "nwb": | ||
| save_nwb(labels, filename, **kwargs) | ||
| elif format == "labelstudio": | ||
| save_labelstudio(labels, filename, **kwargs) | ||
| elif format == "jabs": | ||
| pose_version = kwargs.pop("pose_version", 5) | ||
| save_jabs(labels, pose_version, filename, **kwargs) | ||
| else: | ||
| raise ValueError(f"Unknown format '{format}' for filename: '{filename}'.") |
There was a problem hiding this comment.
Improve the error message in load_file to list supported formats.
- raise ValueError(f"Could not infer format from filename: '{filename}'.")
+ raise ValueError(f"Could not infer format from filename: '{filename}'. Supported formats are: 'slp', 'nwb', 'labelstudio', 'jabs', 'video'.")Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
Suggested change
| def load_file( | |
| filename: str | Path, format: Optional[str] = None, **kwargs | |
| ) -> Union[Labels, Video]: | |
| """Load a file and return the appropriate object. | |
| Args: | |
| filename: Path to a file. | |
| format: Optional format to load as. If not provided, will be inferred from the | |
| file extension. Available formats are: "slp", "nwb", "labelstudio", "jabs" | |
| and "video". | |
| Returns: | |
| A `Labels` or `Video` object. | |
| """ | |
| if isinstance(filename, Path): | |
| filename = str(filename) | |
| if format is None: | |
| if filename.endswith(".slp"): | |
| format = "slp" | |
| elif filename.endswith(".nwb"): | |
| format = "nwb" | |
| elif filename.endswith(".json"): | |
| format = "json" | |
| elif filename.endswith(".h5"): | |
| format = "jabs" | |
| else: | |
| for vid_ext in Video.EXTS: | |
| if filename.endswith(vid_ext): | |
| format = "video" | |
| break | |
| if format is None: | |
| raise ValueError(f"Could not infer format from filename: '{filename}'.") | |
| if filename.endswith(".slp"): | |
| return load_slp(filename, **kwargs) | |
| elif filename.endswith(".nwb"): | |
| return load_nwb(filename, **kwargs) | |
| elif filename.endswith(".json"): | |
| return load_labelstudio(filename, **kwargs) | |
| elif filename.endswith(".h5"): | |
| return load_jabs(filename, **kwargs) | |
| elif format == "video": | |
| return load_video(filename, **kwargs) | |
| def save_file( | |
| labels: Labels, filename: str | Path, format: Optional[str] = None, **kwargs | |
| ): | |
| """Save a file based on the extension. | |
| Args: | |
| labels: A SLEAP `Labels` object (see `load_slp`). | |
| filename: Path to save labels to. | |
| format: Optional format to save as. If not provided, will be inferred from the | |
| file extension. Available formats are: "slp", "nwb", "labelstudio" and | |
| "jabs". | |
| """ | |
| if isinstance(filename, Path): | |
| filename = str(filename) | |
| if format is None: | |
| if filename.endswith(".slp"): | |
| format = "slp" | |
| elif filename.endswith(".nwb"): | |
| format = "nwb" | |
| elif filename.endswith(".json"): | |
| format = "labelstudio" | |
| elif "pose_version" in kwargs: | |
| format = "jabs" | |
| if format == "slp": | |
| save_slp(labels, filename, **kwargs) | |
| elif format == "nwb": | |
| save_nwb(labels, filename, **kwargs) | |
| elif format == "labelstudio": | |
| save_labelstudio(labels, filename, **kwargs) | |
| elif format == "jabs": | |
| pose_version = kwargs.pop("pose_version", 5) | |
| save_jabs(labels, pose_version, filename, **kwargs) | |
| else: | |
| raise ValueError(f"Unknown format '{format}' for filename: '{filename}'.") | |
| def load_file( | |
| filename: str | Path, format: Optional[str] = None, **kwargs | |
| ) -> Union[Labels, Video]: | |
| """Load a file and return the appropriate object. | |
| Args: | |
| filename: Path to a file. | |
| format: Optional format to load as. If not provided, will be inferred from the | |
| file extension. Available formats are: "slp", "nwb", "labelstudio", "jabs" | |
| and "video". | |
| Returns: | |
| A `Labels` or `Video` object. | |
| """ | |
| if isinstance(filename, Path): | |
| filename = str(filename) | |
| if format is None: | |
| if filename.endswith(".slp"): | |
| format = "slp" | |
| elif filename.endswith(".nwb"): | |
| format = "nwb" | |
| elif filename.endswith(".json"): | |
| format = "json" | |
| elif filename.endswith(".h5"): | |
| format = "jabs" | |
| else: | |
| for vid_ext in Video.EXTS: | |
| if filename.endswith(vid_ext): | |
| format = "video" | |
| break | |
| if format is None: | |
| raise ValueError(f"Could not infer format from filename: '{filename}'. Supported formats are: 'slp', 'nwb', 'labelstudio', 'jabs', 'video'.") | |
| if filename.endswith(".slp"): | |
| return load_slp(filename, **kwargs) | |
| elif filename.endswith(".nwb"): | |
| return load_nwb(filename, **kwargs) | |
| elif filename.endswith(".json"): | |
| return load_labelstudio(filename, **kwargs) | |
| elif filename.endswith(".h5"): | |
| return load_jabs(filename, **kwargs) | |
| elif format == "video": | |
| return load_video(filename, **kwargs) | |
| def save_file( | |
| labels: Labels, filename: str | Path, format: Optional[str] = None, **kwargs | |
| ): | |
| """Save a file based on the extension. | |
| Args: | |
| labels: A SLEAP `Labels` object (see `load_slp`). | |
| filename: Path to save labels to. | |
| format: Optional format to save as. If not provided, will be inferred from the | |
| file extension. Available formats are: "slp", "nwb", "labelstudio" and | |
| "jabs". | |
| """ | |
| if isinstance(filename, Path): | |
| filename = str(filename) | |
| if format is None: | |
| if filename.endswith(".slp"): | |
| format = "slp" | |
| elif filename.endswith(".nwb"): | |
| format = "nwb" | |
| elif filename.endswith(".json"): | |
| format = "labelstudio" | |
| elif "pose_version" in kwargs: | |
| format = "jabs" | |
| if format == "slp": | |
| save_slp(labels, filename, **kwargs) | |
| elif format == "nwb": | |
| save_nwb(labels, filename, **kwargs) | |
| elif format == "labelstudio": | |
| save_labelstudio(labels, filename, **kwargs) | |
| elif format == "jabs": | |
| pose_version = kwargs.pop("pose_version", 5) | |
| save_jabs(labels, pose_version, filename, **kwargs) | |
| else: | |
| raise ValueError(f"Unknown format '{format}' for filename: '{filename}'.") |
Comment on lines
+174
to
+209
| def save_file( | ||
| labels: Labels, filename: str | Path, format: Optional[str] = None, **kwargs | ||
| ): | ||
| """Save a file based on the extension. | ||
|
|
||
| Args: | ||
| labels: A SLEAP `Labels` object (see `load_slp`). | ||
| filename: Path to save labels to. | ||
| format: Optional format to save as. If not provided, will be inferred from the | ||
| file extension. Available formats are: "slp", "nwb", "labelstudio" and | ||
| "jabs". | ||
| """ | ||
| if isinstance(filename, Path): | ||
| filename = str(filename) | ||
|
|
||
| if format is None: | ||
| if filename.endswith(".slp"): | ||
| format = "slp" | ||
| elif filename.endswith(".nwb"): | ||
| format = "nwb" | ||
| elif filename.endswith(".json"): | ||
| format = "labelstudio" | ||
| elif "pose_version" in kwargs: | ||
| format = "jabs" | ||
|
|
||
| if format == "slp": | ||
| save_slp(labels, filename, **kwargs) | ||
| elif format == "nwb": | ||
| save_nwb(labels, filename, **kwargs) | ||
| elif format == "labelstudio": | ||
| save_labelstudio(labels, filename, **kwargs) | ||
| elif format == "jabs": | ||
| pose_version = kwargs.pop("pose_version", 5) | ||
| save_jabs(labels, pose_version, filename, **kwargs) | ||
| else: | ||
| raise ValueError(f"Unknown format '{format}' for filename: '{filename}'.") |
There was a problem hiding this comment.
Refactor save_file to handle pose_version more consistently.
- elif "pose_version" in kwargs:
- format = "jabs"
+ # Move pose_version handling to the jabs-specific blockCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
Suggested change
| def save_file( | |
| labels: Labels, filename: str | Path, format: Optional[str] = None, **kwargs | |
| ): | |
| """Save a file based on the extension. | |
| Args: | |
| labels: A SLEAP `Labels` object (see `load_slp`). | |
| filename: Path to save labels to. | |
| format: Optional format to save as. If not provided, will be inferred from the | |
| file extension. Available formats are: "slp", "nwb", "labelstudio" and | |
| "jabs". | |
| """ | |
| if isinstance(filename, Path): | |
| filename = str(filename) | |
| if format is None: | |
| if filename.endswith(".slp"): | |
| format = "slp" | |
| elif filename.endswith(".nwb"): | |
| format = "nwb" | |
| elif filename.endswith(".json"): | |
| format = "labelstudio" | |
| elif "pose_version" in kwargs: | |
| format = "jabs" | |
| if format == "slp": | |
| save_slp(labels, filename, **kwargs) | |
| elif format == "nwb": | |
| save_nwb(labels, filename, **kwargs) | |
| elif format == "labelstudio": | |
| save_labelstudio(labels, filename, **kwargs) | |
| elif format == "jabs": | |
| pose_version = kwargs.pop("pose_version", 5) | |
| save_jabs(labels, pose_version, filename, **kwargs) | |
| else: | |
| raise ValueError(f"Unknown format '{format}' for filename: '{filename}'.") | |
| def save_file( | |
| labels: Labels, filename: str | Path, format: Optional[str] = None, **kwargs | |
| ): | |
| """Save a file based on the extension. | |
| Args: | |
| labels: A SLEAP `Labels` object (see `load_slp`). | |
| filename: Path to save labels to. | |
| format: Optional format to save as. If not provided, will be inferred from the | |
| file extension. Available formats are: "slp", "nwb", "labelstudio" and | |
| "jabs". | |
| """ | |
| if isinstance(filename, Path): | |
| filename = str(filename) | |
| if format is None: | |
| if filename.endswith(".slp"): | |
| format = "slp" | |
| elif filename.endswith(".nwb"): | |
| format = "nwb" | |
| elif filename.endswith(".json"): | |
| format = "labelstudio" | |
| # Move pose_version handling to the jabs-specific block | |
| if format == "slp": | |
| save_slp(labels, filename, **kwargs) | |
| elif format == "nwb": | |
| save_nwb(labels, filename, **kwargs) | |
| elif format == "labelstudio": | |
| save_labelstudio(labels, filename, **kwargs) | |
| elif format == "jabs": | |
| pose_version = kwargs.pop("pose_version", 5) | |
| save_jabs(labels, pose_version, filename, **kwargs) | |
| else: | |
| raise ValueError(f"Unknown format '{format}' for filename: '{filename}'.") |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
load_videoandload_filehigh level APIsSummary by CodeRabbit