AI Toolkit for Healthcare Imaging
This report summarizes scanner evidence for Project-MONAI/MONAI, a Python project with 8,763 GitHub stars. SynthScan examined 286,966 lines of code across 1451 source files, recording 5570 pattern matches distributed across 21 syntactic categories. The legacy adjusted pattern signal is 21.3 (Elevated pattern signal); it is not an authorship estimate.
Use the findings to ask whether maintainers can explain intent, verify dependencies, simplify unnecessary scaffolding, and focus review effort. Risk Payload v1 adds ownership, supply-chain, over-engineering, and review-effort vectors when available. These are prompts for human verification, not probabilities, security findings, or measured maintenance costs.
Use each vector to guide manual verification of the underlying findings.
Can maintainers explain intent, assumptions, and trade-offs? 2014 finding(s).
Are imports declared and package/API names verified? 3071 finding(s).
Are wrappers, guards, and repeated structures necessary? 1900 finding(s).
Which changes need focused human review? 5570 finding(s).
This chart tracks the legacy adjusted pattern score across scan runs. Changes can reflect source changes, scan coverage, or detector/scoring versions; they do not measure AI adoption or prove that a team refactored code. Compare runs only when their scoring versions are compatible. The dashed line tracks the raw pattern-hit count.
Groups findings by configured severity weight. Severity is not a confidence estimate, security rating, or proof that a package is missing. Verify imports against the project's manifests and inspect each finding in its local design context.
This horizontal bar chart shows where configured pattern scores accumulate across directories. Treat the bars as locations to inspect, not as evidence of authorship or code quality. Use the file-level findings to decide whether a directory needs a focused ownership, dependency, complexity, or review check.
The scanner identified 5570 distinct pattern matches across 21 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a detector match to inspect in context. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.
Reading the findings table: The Severity column indicates the configured finding weight (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — legacy comment-context matches receive a ×1.5 score weight. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier under the legacy scoring model.
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | setup.py | 12 | CODE | |
| LOW | monai/__init__.py | 12 | CODE | |
| LOW | monai/metrics/generalized_dice.py | 12 | CODE | |
| LOW | monai/metrics/loss_metric.py | 12 | CODE | |
| LOW | monai/metrics/wrapper.py | 12 | CODE | |
| LOW | monai/metrics/meandice.py | 12 | CODE | |
| LOW | monai/metrics/f_beta_score.py | 12 | CODE | |
| LOW | monai/metrics/regression.py | 12 | CODE | |
| LOW | monai/metrics/absolute_volume_difference.py | 12 | CODE | |
| LOW | monai/metrics/embedding_collapse.py | 12 | CODE | |
| LOW | monai/metrics/cumulative_average.py | 12 | CODE | |
| LOW | monai/metrics/__init__.py | 12 | CODE | |
| LOW | monai/metrics/__init__.py | 14 | CODE | |
| LOW | monai/metrics/__init__.py | 14 | CODE | |
| LOW | monai/metrics/__init__.py | 15 | CODE | |
| LOW | monai/metrics/__init__.py | 15 | CODE | |
| LOW | monai/metrics/__init__.py | 15 | CODE | |
| LOW | monai/metrics/__init__.py | 15 | CODE | |
| LOW | monai/metrics/__init__.py | 16 | CODE | |
| LOW | monai/metrics/__init__.py | 16 | CODE | |
| LOW | monai/metrics/__init__.py | 17 | CODE | |
| LOW | monai/metrics/__init__.py | 17 | CODE | |
| LOW | monai/metrics/__init__.py | 17 | CODE | |
| LOW | monai/metrics/__init__.py | 18 | CODE | |
| LOW | monai/metrics/__init__.py | 18 | CODE | |
| LOW | monai/metrics/__init__.py | 18 | CODE | |
| LOW | monai/metrics/__init__.py | 19 | CODE | |
| LOW | monai/metrics/__init__.py | 20 | CODE | |
| LOW | monai/metrics/__init__.py | 20 | CODE | |
| LOW | monai/metrics/__init__.py | 21 | CODE | |
| LOW | monai/metrics/__init__.py | 22 | CODE | |
| LOW | monai/metrics/__init__.py | 22 | CODE | |
| LOW | monai/metrics/__init__.py | 23 | CODE | |
| LOW | monai/metrics/__init__.py | 23 | CODE | |
| LOW | monai/metrics/__init__.py | 23 | CODE | |
| LOW | monai/metrics/__init__.py | 23 | CODE | |
| LOW | monai/metrics/__init__.py | 24 | CODE | |
| LOW | monai/metrics/__init__.py | 24 | CODE | |
| LOW | monai/metrics/__init__.py | 25 | CODE | |
| LOW | monai/metrics/__init__.py | 25 | CODE | |
| LOW | monai/metrics/__init__.py | 26 | CODE | |
| LOW | monai/metrics/__init__.py | 27 | CODE | |
| LOW | monai/metrics/__init__.py | 27 | CODE | |
| LOW | monai/metrics/__init__.py | 27 | CODE | |
| LOW | monai/metrics/__init__.py | 28 | CODE | |
| LOW | monai/metrics/__init__.py | 28 | CODE | |
| LOW | monai/metrics/__init__.py | 29 | CODE | |
| LOW | monai/metrics/__init__.py | 29 | CODE | |
| LOW | monai/metrics/__init__.py | 29 | CODE | |
| LOW | monai/metrics/__init__.py | 29 | CODE | |
| LOW | monai/metrics/__init__.py | 30 | CODE | |
| LOW | monai/metrics/__init__.py | 30 | CODE | |
| LOW | monai/metrics/__init__.py | 31 | CODE | |
| LOW | monai/metrics/__init__.py | 31 | CODE | |
| LOW | monai/metrics/__init__.py | 32 | CODE | |
| LOW | monai/metrics/__init__.py | 32 | CODE | |
| LOW | monai/metrics/__init__.py | 32 | CODE | |
| LOW | monai/metrics/__init__.py | 32 | CODE | |
| LOW | monai/metrics/__init__.py | 32 | CODE | |
| LOW | monai/metrics/__init__.py | 32 | CODE | |
| 2995 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | versioneer.py | 692 | def git_versions_from_keywords( | CODE |
| LOW | versioneer.py | 1223 | def git_versions_from_keywords( | STRING |
| LOW | monai/_version.py | 185 | def git_versions_from_keywords( | CODE |
| LOW | monai/metrics/regression.py | 249 | def compute_mean_error_metrics(y_pred: torch.Tensor, y: torch.Tensor, func: Callable) -> torch.Tensor: | STRING |
| LOW | monai/metrics/absolute_volume_difference.py | 133 | def compute_absolute_volume_difference( | CODE |
| LOW | monai/metrics/embedding_collapse.py | 129 | def compute_embedding_collapse( | CODE |
| LOW | monai/metrics/surface_distance.py | 141 | def compute_average_surface_distance( | CODE |
| LOW | monai/metrics/panoptic_quality.py | 303 | def _check_panoptic_metric_name(metric_name: str) -> str: | CODE |
| LOW | monai/metrics/average_precision.py | 118 | def compute_average_precision( | CODE |
| LOW | monai/metrics/utils.py | 381 | def get_edge_surface_distance( | CODE |
| LOW | monai/metrics/utils.py | 601 | def compute_voronoi_regions_fast(labels: np.ndarray | torch.Tensor) -> torch.Tensor: | CODE |
| LOW | monai/metrics/utils.py | 659 | def _get_neighbour_code_to_normals_table(device=None): | CODE |
| LOW | monai/metrics/utils.py | 932 | def create_table_neighbour_code_to_surface_area(spacing_mm, device=None): | CODE |
| LOW | monai/metrics/utils.py | 961 | def create_table_neighbour_code_to_contour_length(spacing_mm, device=None): | CODE |
| LOW | monai/metrics/utils.py | 1003 | def get_code_to_measure_table(spacing, device=None): | CODE |
| LOW | monai/metrics/hausdorff_distance.py | 152 | def compute_hausdorff_distance( | CODE |
| LOW | monai/metrics/hausdorff_distance.py | 247 | def _compute_percentile_hausdorff_distance( | CODE |
| LOW | monai/metrics/confusion_matrix.py | 220 | def compute_confusion_matrix_metric(metric_name: str, confusion_matrix: torch.Tensor) -> torch.Tensor: | CODE |
| LOW | monai/metrics/confusion_matrix.py | 315 | def check_confusion_matrix_metric_name(metric_name: str) -> str: | CODE |
| LOW | monai/losses/perceptual.py | 321 | def medicalnet_intensity_normalisation(volume): | CODE |
| LOW | monai/losses/dice.py | 664 | def _compute_generalized_true_positive( | CODE |
| LOW | monai/losses/dice.py | 700 | def _compute_alpha_generalized_true_positives(self, flat_target: torch.Tensor) -> torch.Tensor: | CODE |
| LOW | monai/losses/image_dissimilarity.py | 273 | def parzen_windowing_b_spline(self, img: torch.Tensor, order: int) -> tuple[torch.Tensor, torch.Tensor]: | CODE |
| LOW | monai/losses/image_dissimilarity.py | 333 | def parzen_windowing_gaussian(self, img: torch.Tensor) -> tuple[torch.Tensor, torch.Tensor]: | CODE |
| LOW | monai/auto3dseg/utils.py | 572 | def list_to_python_fire_arg_str(args: list) -> str: | CODE |
| LOW | monai/auto3dseg/utils.py | 586 | def check_and_set_optional_args(params: dict) -> str: | CODE |
| LOW | monai/config/deviceconfig.py | 77 | def get_optional_config_values(): | CODE |
| LOW | monai/fl/client/monai_algo.py | 38 | def _warn_provisioned_config_execution(bundle_root: str) -> None: | CODE |
| LOW | monai/bundle/config_parser.py | 565 | def resolve_macro_and_relative_ids(self): | CODE |
| LOW | monai/bundle/config_item.py | 73 | def _find_classes_or_functions(self, modnames: Sequence[str] | str) -> dict[str, list]: | CODE |
| LOW | monai/bundle/config_item.py | 96 | def get_component_module_name(self, name: str) -> list[str] | str | None: | CODE |
| LOW | monai/bundle/workflows.py | 46 | def _reject_executable_logging_config(logging_file: str) -> str: | CODE |
| LOW | monai/bundle/workflows.py | 104 | def _is_allowed_logging_class(module: str, attribute: str) -> bool: | CODE |
| LOW | monai/bundle/workflows.py | 123 | def _reject_non_logging_class(value: str, logging_file: str, section: str) -> None: | CODE |
| LOW | monai/bundle/workflows.py | 177 | def _reject_non_literal_expression(value: str, logging_file: str, section: str, field: str) -> None: | CODE |
| LOW⚡ | monai/bundle/scripts.py | 181 | def _get_ngc_private_base_url(repo: str) -> str: | CODE |
| LOW⚡ | monai/bundle/scripts.py | 185 | def _get_ngc_private_bundle_url(model_name: str, version: str, repo: str) -> str: | CODE |
| LOW⚡ | monai/bundle/scripts.py | 189 | def _get_monaihosting_bundle_url(model_name: str, version: str) -> str: | CODE |
| LOW | monai/bundle/scripts.py | 203 | def _download_from_monaihosting(download_path: Path, filename: str, version: str, progress: bool) -> None: | CODE |
| LOW | monai/bundle/scripts.py | 210 | def _download_from_bundle_info(download_path: Path, filename: str, version: str, progress: bool) -> None: | CODE |
| LOW | monai/bundle/scripts.py | 266 | def _download_from_ngc_private( | CODE |
| LOW | monai/bundle/scripts.py | 379 | def _get_latest_bundle_version_ngc(name: str, repo: str | None = None, headers: dict | None = None) -> str: | CODE |
| LOW | monai/bundle/scripts.py | 410 | def _get_latest_bundle_version( | CODE |
| LOW | monai/utils/misc.py | 874 | def _calculate_conversion_factor(self): | CODE |
| LOW | monai/utils/misc.py | 886 | def check_kwargs_exist_in_class_init(cls, kwargs): | CODE |
| LOW | monai/utils/type_conversion.py | 47 | def get_numpy_dtype_from_string(dtype: str) -> np.dtype: | CODE |
| LOW | monai/utils/type_conversion.py | 52 | def get_torch_dtype_from_string(dtype: str) -> torch.dtype: | CODE |
| LOW | monai/utils/ordering.py | 97 | def get_revert_sequence_ordering(self) -> np.ndarray: | CODE |
| LOW | monai/utils/module.py | 145 | def damerau_levenshtein_distance(s1: str, s2: str) -> int: | CODE |
| LOW | monai/utils/module.py | 646 | def compute_capabilities_after(major: int, minor: int = 0, current_ver_string: str | None = None) -> bool: | CODE |
| LOW⚡ | monai/utils/dist.py | 48 | def evenly_divisible_all_gather(data: torch.Tensor, concat: Literal[True]) -> torch.Tensor: ... | CODE |
| LOW⚡ | monai/utils/dist.py | 52 | def evenly_divisible_all_gather(data: torch.Tensor, concat: Literal[False]) -> list[torch.Tensor]: ... | CODE |
| LOW⚡ | monai/utils/dist.py | 56 | def evenly_divisible_all_gather(data: torch.Tensor, concat: bool) -> torch.Tensor | list[torch.Tensor]: ... | CODE |
| LOW⚡ | monai/utils/dist.py | 59 | def evenly_divisible_all_gather(data: torch.Tensor, concat: bool = True) -> torch.Tensor | list[torch.Tensor]: | CODE |
| LOW | monai/utils/profiling.py | 70 | def torch_profiler_time_cpu_gpu(func): | CODE |
| LOW | monai/utils/profiling.py | 95 | def torch_profiler_time_end_to_end(func): | CODE |
| LOW | monai/visualize/class_activation_maps.py | 208 | def _upsample_and_post_process(self, acti_map, x): | CODE |
| LOW | monai/visualize/img2tensorboard.py | 80 | def make_animated_gif_summary( | CODE |
| LOW | monai/inferers/splitter.py | 194 | def _get_valid_shape_parameters( | CODE |
| LOW | monai/inferers/inferer.py | 867 | def _scheduler_step_supports_kwarg(scheduler: Scheduler, kwarg: str) -> bool: | CODE |
| 1083 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | monai/metrics/generalized_dice.py | 76 | Computes the Generalized Dice Score and returns a tensor with its per image values. Args: | STRING |
| HIGH | monai/metrics/generalized_dice.py | 137 | Computes the Generalized Dice Score and returns a tensor with its per image values. Args: y_pred (torc | STRING |
| HIGH | monai/metrics/absolute_volume_difference.py | 136 | Compute the Absolute Volume Difference (AVD) for a batch of segmentation predictions. AVD is defined per class | STRING |
| HIGH | monai/metrics/embedding_collapse.py | 97 | Compute collapse scores. Args: embeddings: float tensor of shape ``[N, D]``. Required. | STRING |
| HIGH | monai/metrics/embedding_collapse.py | 137 | Functional form of :class:`EmbeddingCollapseMetric`. Computes a suite of representational collapse indicators from | STRING |
| HIGH | monai/metrics/embedding_collapse.py | 426 | Fit a linear classifier on embeddings and return test accuracy. Used to validate that collapse scores predict downs | STRING |
| HIGH | monai/metrics/utils.py | 541 | This function is used to prepare the `spacing` parameter to include batch dimension for the computation of surf | STRING |
| HIGH | monai/metrics/utils.py | 602 | Voronoi assignment to connected components (CPU, single EDT) without cc3d. Returns the ID of the nearest compon | STRING |
| HIGH | monai/metrics/hausdorff_distance.py | 162 | Compute the Hausdorff distance. Args: y_pred: input data to compute, typical segmentation model output | STRING |
| HIGH | monai/metrics/hausdorff_distance.py | 250 | Reduce a tensor of surface distances to a single Hausdorff distance. Args: surface_distance: the surfa | STRING |
| HIGH | monai/metrics/meaniou.py | 122 | Computes Intersection over Union (IoU) score metric from a batch of predictions. Args: y_pred: input data t | STRING |
| HIGH | monai/metrics/surface_dice.py | 92 | Args: y_pred: Predicted segmentation, typically segmentation model output. It must | STRING |
| HIGH | monai/metrics/surface_dice.py | 161 | This function computes the (Normalized) Surface Dice (NSD) between the two tensors `y_pred` (referred to as :ma | STRING |
| HIGH | monai/metrics/calibration.py | 29 | Compute calibration bins for predicted probabilities and ground truth labels. This function implements hard bi | STRING |
| HIGH | monai/losses/ds_loss.py | 72 | Args: input: a single tensor or a list of tensors from deeply supervised network outputs. | STRING |
| HIGH | monai/losses/dice.py | 845 | Args: input: the shape should be BNH[WD]. target: the shape should be BNH[WD] or B1H[WD | STRING |
| HIGH | monai/losses/dice.py | 977 | Args: input: the shape should be BNH[WD]. The input should be the original logits d | STRING |
| HIGH | monai/losses/dice.py | 1099 | Args: input (torch.Tensor): the shape should be BNH[WD]. The input should be the original logits | STRING |
| HIGH | monai/losses/aucm_loss.py | 91 | Args: input: the shape should be B1HW[D], where the channel dimension is 1 for binary classificatio | STRING |
| HIGH | monai/losses/hausdorff_loss.py | 229 | Compute the logarithm of the Hausdorff Distance Transform Loss. Args: input (torch.Tensor) | STRING |
| HIGH | monai/auto3dseg/analyzer.py | 175 | Analyzer to extract image stats properties for each case(image). Args: image_key: the key to find imag | STRING |
| HIGH | monai/auto3dseg/analyzer.py | 426 | Callable to execute the pre-defined functions. Returns: A dictionary. The dict has the key | STRING |
| HIGH | monai/auto3dseg/analyzer.py | 587 | Callable to execute the pre-defined functions Returns: A dictionary. The dict has the key | STRING |
| HIGH | monai/auto3dseg/analyzer.py | 665 | Callable to execute the pre-defined functions. Returns: A dictionary. The dict has the key | STRING |
| HIGH | monai/auto3dseg/analyzer.py | 754 | Callable to execute the pre-defined functions Returns: A dictionary. The dict has the key | STRING |
| HIGH | monai/auto3dseg/analyzer.py | 1008 | Callable to execute the pre-defined functions Returns: A dictionary. The dict has the key | STRING |
| HIGH | monai/auto3dseg/seg_summarizer.py | 174 | Summarize the input list of data and generates a report ready for json/yaml export. Args: | STRING |
| HIGH | monai/auto3dseg/utils.py | 107 | Get a foreground image by removing all-zero rectangles on the edges of the image Note for the developer: update | STRING |
| HIGH | monai/auto3dseg/utils.py | 461 | Import the Algo object from a JSON file (pickle-free serialization). Args: filename: the name of the s | STRING |
| HIGH | monai/auto3dseg/utils.py | 599 | Prepare the command for subprocess to run the script with the given arguments. Args: cmd: the command | STRING |
| HIGH | monai/auto3dseg/utils.py | 630 | Prepare the command for multi-gpu/multi-node job execution using torchrun. Args: cmd: the command or s | STRING |
| HIGH | monai/auto3dseg/utils.py | 652 | Prepare the command for distributed job running using bcprun. Args: script: the script to run in the d | STRING |
| HIGH | monai/bundle/config_parser.py | 134 | Resolve ``key`` as a nested config id. Args: key: the child key/index. Returns: | STRING |
| HIGH | monai/bundle/workflows.py | 47 | Reject a logging INI whose ``class=``/``args=`` fields would execute arbitrary code. `logging.config.fileConfi | STRING |
| HIGH | monai/bundle/scripts.py | 1890 | Push a MONAI bundle to the Hugging Face Hub. Typical usage examples: .. code-block:: bash python | STRING |
| HIGH | monai/utils/safeeval.py | 67 | Evaluate the Python expression `expr` using `eval`, but only if it is a safe expression in that its parsed AST | STRING |
| HIGH | monai/utils/misc.py | 232 | Given a dictionary whose values contain scalars or tuples (with the same length as ``keys``), Create a dictiona | STRING |
| HIGH | monai/utils/module.py | 327 | Imports an optional module specified by `module` string. Any importing related exceptions will be stored, and e | STRING |
| HIGH | monai/inferers/merger.py | 498 | Iterate over chunks of a given shape. Args: chunks: the chunk shape cdata_shape: the shape of | STRING |
| HIGH | monai/networks/utils.py | 368 | Apply pixel shuffle to the tensor `x` with spatial dimensions `spatial_dims` and scaling factor `scale_factor`. | STRING |
| HIGH | monai/networks/utils.py | 413 | Apply pixel unshuffle to the tensor `x` with spatial dimensions `spatial_dims` and scaling factor `scale_factor`. | STRING |
| HIGH | monai/networks/utils.py | 548 | Compute a module state_dict, of which the keys are the same as `dst`. The values of `dst` are overwritten by th | STRING |
| HIGH | monai/networks/utils.py | 1140 | Replace sub-module(s) in a parent module. The name of the module to be replace can be nested e.g., `featur | STRING |
| HIGH | monai/networks/layers/simplelayers.py | 208 | Apply 1-D convolutions along each spatial dimension of `x`. Args: x: the input image. must have shape | STRING |
| HIGH | monai/networks/layers/simplelayers.py | 253 | Filtering `x` with `kernel` independently for each batch and channel respectively. Args: x: the input | STRING |
| HIGH | monai/networks/layers/convutils.py | 81 | one dimensional Gaussian kernel. Args: sigma: std of the kernel truncated: tail length | STRING |
| HIGH | monai/networks/layers/factories.py | 164 | Split arguments in a way to be suitable for using with the factory types. If `args` is a string it's interpreted as | STRING |
| HIGH | monai/networks/nets/mednext.py | 277 | Factory method to create MedNeXt variants. Args: variant (str): The MedNeXt variant to create ('S', 'B | STRING |
| HIGH | monai/networks/nets/navit.py | 222 | NaViT: Native Resolution Vision Transformer with Patch n' Pack, extended to 2D and 3D. Based on: "Dehghani et al., | STRING |
| HIGH | monai/networks/nets/navit.py | 435 | Run NaViT on a batch of packed image groups. Args: batched_images: a list of groups, where each gro | STRING |
| HIGH | monai/networks/nets/efficientnet.py | 961 | Get a BlockArgs object from a string notation of arguments. Args: block_string (str): A st | STRING |
| HIGH | monai/networks/nets/quicknat.py | 46 | Combine the input with the indexed submodule output. Args: input: input tensor for the skip connect | STRING |
| HIGH | monai/networks/nets/resnet.py | 621 | Download resnet pretrained weights from https://huggingface.co/TencentMedicalNet Args: resnet_depth: d | STRING |
| HIGH | monai/networks/nets/hyena_nd_unetr.py | 116 | Build a :class:`HyenaNDUNETR` matching one of the NeurIPS 2026 paper variants. Args: variant: one o | STRING |
| HIGH | monai/networks/nets/swin_unetr.py | 103 | Args: in_channels: dimension of input channels. out_channels: dimension of output chann | STRING |
| HIGH | monai/transforms/utils.py | 1629 | Generate extreme points from an image. These are used to generate initial segmentation for annotation models. A | STRING |
| HIGH | monai/transforms/transform.py | 54 | Perform a transform 'transform' on 'data', according to the other parameters specified. If `data` is a tuple a | STRING |
| HIGH | monai/transforms/transform.py | 112 | Transform `data` with `transform`. If `data` is a list or tuple and `map_data` is True, each item of `data` wi | STRING |
| HIGH | monai/transforms/transform.py | 203 | Set the random state locally, to control the randomness, the derived classes should use :py:attr:`self. | STRING |
| HIGH | monai/transforms/inverse.py | 345 | Get most recent matching transform for the current class from the sequence of applied operations. Args | STRING |
| 36 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | monai/metrics/embedding_collapse.py | 231 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | monai/metrics/embedding_collapse.py | 233 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | monai/metrics/embedding_collapse.py | 414 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | monai/metrics/embedding_collapse.py | 416 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | monai/inferers/utils.py | 157 | # ----------------------------------------------------------------- | COMMENT |
| MEDIUM | monai/networks/blocks/backbone_fpn_utils.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/blocks/feature_pyramid_network.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM⚡ | monai/networks/blocks/hyena.py | 76 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | monai/networks/blocks/hyena.py | 78 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | monai/networks/blocks/hyena.py | 230 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | monai/networks/blocks/hyena.py | 232 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | monai/networks/blocks/hyena.py | 427 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | monai/networks/blocks/hyena.py | 429 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | monai/networks/nets/diffusion_model_unet.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/nets/diffusion_model_unet.py | 30 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/nets/hovernet.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/nets/hovernet.py | 28 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/nets/controlnet.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/nets/controlnet.py | 30 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/nets/spade_diffusion_model_unet.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/nets/spade_diffusion_model_unet.py | 30 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/schedulers/ddim.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/schedulers/ddim.py | 30 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/schedulers/pndm.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/schedulers/pndm.py | 30 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/schedulers/rectified_flow.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/schedulers/rectified_flow.py | 27 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/schedulers/scheduler.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/schedulers/scheduler.py | 30 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/schedulers/ddpm.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/networks/schedulers/ddpm.py | 30 | # ========================================================================= | COMMENT |
| MEDIUM | monai/data/image_reader.py | 826 | # ========================================================================= | STRING |
| MEDIUM | monai/data/image_reader.py | 846 | # ========================================================================= | STRING |
| MEDIUM | monai/apps/detection/metrics/coco.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/apps/detection/metrics/coco.py | 28 | # ========================================================================= | COMMENT |
| MEDIUM | monai/apps/detection/metrics/matching.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/apps/detection/metrics/matching.py | 28 | # ========================================================================= | COMMENT |
| MEDIUM | monai/apps/detection/utils/hard_negative_sampler.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/apps/detection/utils/box_coder.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/apps/detection/utils/box_selector.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/apps/detection/utils/anchor_utils.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/apps/detection/utils/ATSS_matcher.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/apps/detection/utils/ATSS_matcher.py | 28 | # ========================================================================= | COMMENT |
| MEDIUM | monai/apps/detection/networks/retinanet_network.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | monai/apps/detection/networks/retinanet_detector.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | …eneration/maisi/networks/diffusion_model_unet_maisi.py | 12 | # ========================================================================= | COMMENT |
| MEDIUM | …eneration/maisi/networks/diffusion_model_unet_maisi.py | 30 | # ========================================================================= | COMMENT |
| MEDIUM | tests/losses/test_aucm_loss.py | 26 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | tests/losses/test_aucm_loss.py | 28 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | tests/losses/test_aucm_loss.py | 44 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | tests/losses/test_aucm_loss.py | 46 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | tests/losses/test_aucm_loss.py | 57 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | tests/losses/test_aucm_loss.py | 59 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | tests/losses/test_aucm_loss.py | 70 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | tests/losses/test_aucm_loss.py | 72 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | tests/losses/test_aucm_loss.py | 83 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | tests/losses/test_aucm_loss.py | 85 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | tests/losses/test_aucm_loss.py | 96 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | tests/losses/test_aucm_loss.py | 98 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | tests/losses/test_aucm_loss.py | 100 | # ------------------------------------------------------------------ | COMMENT |
| 31 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
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| LOW | monai/metrics/meandice.py | 126 | CODE | |
| LOW | monai/metrics/meandice.py | 302 | CODE | |
| LOW | monai/metrics/regression.py | 307 | CODE | |
| LOW | monai/metrics/regression.py | 508 | CODE | |
| LOW | monai/losses/perceptual.py | 88 | CODE | |
| LOW | monai/losses/dice.py | 56 | CODE | |
| LOW | monai/losses/dice.py | 256 | CODE | |
| LOW | monai/losses/dice.py | 338 | CODE | |
| LOW | monai/losses/dice.py | 728 | CODE | |
| LOW | monai/losses/dice.py | 890 | CODE | |
| LOW | monai/losses/dice.py | 1054 | CODE | |
| LOW | monai/losses/tversky.py | 41 | CODE | |
| LOW | monai/losses/mcc_loss.py | 54 | CODE | |
| LOW | monai/losses/focal_loss.py | 69 | CODE | |
| LOW | monai/losses/cldice.py | 120 | CODE | |
| LOW | monai/losses/cldice.py | 270 | CODE | |
| LOW | monai/losses/hausdorff_loss.py | 44 | CODE | |
| LOW | monai/losses/calibration.py | 260 | CODE | |
| LOW | monai/losses/calibration.py | 344 | CODE | |
| LOW | monai/fl/client/monai_algo.py | 397 | CODE | |
| LOW | monai/bundle/workflows.py | 627 | CODE | |
| LOW | monai/bundle/scripts.py | 449 | CODE | |
| LOW | monai/bundle/scripts.py | 631 | CODE | |
| LOW | monai/bundle/scripts.py | 935 | CODE | |
| LOW | monai/bundle/scripts.py | 1176 | CODE | |
| LOW | monai/bundle/scripts.py | 1341 | CODE | |
| LOW | monai/bundle/scripts.py | 1456 | CODE | |
| LOW | monai/bundle/scripts.py | 1590 | CODE | |
| LOW | monai/visualize/utils.py | 34 | CODE | |
| LOW | monai/optimizers/lr_finder.py | 256 | CODE | |
| LOW | monai/inferers/utils.py | 42 | CODE | |
| LOW | monai/inferers/inferer.py | 131 | CODE | |
| LOW | monai/inferers/inferer.py | 503 | CODE | |
| LOW | monai/inferers/inferer.py | 999 | CODE | |
| LOW | monai/inferers/inferer.py | 1096 | CODE | |
| LOW | monai/inferers/inferer.py | 1356 | CODE | |
| LOW | monai/inferers/inferer.py | 1443 | CODE | |
| LOW | monai/inferers/inferer.py | 1576 | CODE | |
| LOW | monai/inferers/inferer.py | 1706 | CODE | |
| LOW | monai/inferers/inferer.py | 1948 | CODE | |
| LOW | monai/inferers/inferer.py | 2045 | CODE | |
| LOW | monai/inferers/merger.py | 263 | CODE | |
| LOW | monai/networks/utils.py | 659 | CODE | |
| LOW | monai/networks/utils.py | 798 | CODE | |
| LOW | monai/networks/utils.py | 942 | CODE | |
| LOW | monai/networks/utils.py | 1328 | CODE | |
| LOW | monai/networks/utils.py | 1350 | CODE | |
| LOW | monai/networks/trt_compiler.py | 313 | CODE | |
| LOW | monai/networks/blocks/crossattention.py | 32 | CODE | |
| LOW | monai/networks/blocks/cablock.py | 138 | CODE | |
| LOW | monai/networks/blocks/downsample.py | 88 | CODE | |
| LOW | monai/networks/blocks/crf.py | 38 | CODE | |
| LOW | monai/networks/blocks/dints_block.py | 136 | CODE | |
| LOW | monai/networks/blocks/convolutions.py | 98 | CODE | |
| LOW | monai/networks/blocks/convolutions.py | 248 | CODE | |
| LOW | monai/networks/blocks/upsample.py | 43 | CODE | |
| LOW | monai/networks/blocks/feature_pyramid_network.py | 265 | CODE | |
| LOW | monai/networks/blocks/transformerblock.py | 33 | CODE | |
| LOW | monai/networks/blocks/hyena.py | 285 | CODE | |
| LOW | monai/networks/blocks/hyena.py | 468 | CODE | |
| 212 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | monai/metrics/regression.py | 0 | execute reduction logic for the output of `compute_iou`. args: reduction: define mode of reduction to the metrics, will | STRING |
| HIGH | monai/metrics/surface_distance.py | 0 | execute reduction logic for the output of `compute_iou`. args: reduction: define mode of reduction to the metrics, will | STRING |
| HIGH | monai/metrics/hausdorff_distance.py | 0 | execute reduction logic for the output of `compute_iou`. args: reduction: define mode of reduction to the metrics, will | STRING |
| HIGH | monai/metrics/meaniou.py | 0 | execute reduction logic for the output of `compute_iou`. args: reduction: define mode of reduction to the metrics, will | STRING |
| HIGH | monai/losses/dice.py | 0 | args: pred: the shape should be bnh[wd]. target: the shape should be bnh[wd]. raises: valueerror: when ``self.reduction` | STRING |
| HIGH | monai/losses/tversky.py | 0 | args: pred: the shape should be bnh[wd]. target: the shape should be bnh[wd]. raises: valueerror: when ``self.reduction` | STRING |
| HIGH | monai/losses/image_dissimilarity.py | 0 | args: pred: the shape should be bnh[wd]. target: the shape should be bnh[wd]. raises: valueerror: when ``self.reduction` | STRING |
| HIGH | monai/networks/blocks/mlp.py | 0 | a self-attention block, based on: "dosovitskiy et al., an image is worth 16x16 words: transformers for image recognition | STRING |
| HIGH | monai/networks/blocks/transformerblock.py | 0 | a self-attention block, based on: "dosovitskiy et al., an image is worth 16x16 words: transformers for image recognition | STRING |
| HIGH | monai/networks/blocks/selfattention.py | 0 | a self-attention block, based on: "dosovitskiy et al., an image is worth 16x16 words: transformers for image recognition | STRING |
| HIGH | monai/networks/nets/diffusion_model_unet.py | 0 | load a state dict from a decoderonlytransformer trained with [monai generative](https://github.com/project-monai/generat | STRING |
| HIGH | monai/networks/nets/controlnet.py | 0 | load a state dict from a decoderonlytransformer trained with [monai generative](https://github.com/project-monai/generat | STRING |
| HIGH | monai/networks/nets/transformer.py | 0 | load a state dict from a decoderonlytransformer trained with [monai generative](https://github.com/project-monai/generat | STRING |
| HIGH | monai/networks/nets/masked_autoencoder_vit.py | 0 | load a state dict from a vitautoenc model trained with an older version of monai where ``crossattentionblock`` was uncon | STRING |
| HIGH | monai/networks/nets/vit.py | 0 | load a state dict from a vitautoenc model trained with an older version of monai where ``crossattentionblock`` was uncon | STRING |
| HIGH | monai/networks/nets/vitautoenc.py | 0 | load a state dict from a vitautoenc model trained with an older version of monai where ``crossattentionblock`` was uncon | STRING |
| HIGH | monai/networks/schedulers/ddim.py | 0 | sets the discrete timesteps used for the diffusion chain. supporting function to be run before inference. args: num_infe | STRING |
| HIGH | monai/networks/schedulers/pndm.py | 0 | sets the discrete timesteps used for the diffusion chain. supporting function to be run before inference. args: num_infe | STRING |
| HIGH | monai/networks/schedulers/ddpm.py | 0 | sets the discrete timesteps used for the diffusion chain. supporting function to be run before inference. args: num_infe | STRING |
| HIGH | monai/apps/detection/utils/box_selector.py | 0 | part of this script is adapted from https://github.com/pytorch/vision/blob/main/torchvision/models/detection/retinanet.p | STRING |
| HIGH | monai/apps/detection/networks/retinanet_network.py | 0 | part of this script is adapted from https://github.com/pytorch/vision/blob/main/torchvision/models/detection/retinanet.p | STRING |
| HIGH | monai/apps/detection/networks/retinanet_detector.py | 0 | part of this script is adapted from https://github.com/pytorch/vision/blob/main/torchvision/models/detection/retinanet.p | STRING |
| HIGH | monai/handlers/earlystop_handler.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/metric_logger.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/classification_saver.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/smartcache_handler.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/lr_schedule_handler.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/tensorboard_handlers.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/trt_handler.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/checkpoint_saver.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/checkpoint_loader.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/metrics_saver.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/postprocessing.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/validation_handler.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/probability_maps.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/decollate_batch.py | 0 | args: engine: ignite engine, it can be a trainer, validator or evaluator. | STRING |
| HIGH | monai/handlers/tensorboard_handlers.py | 0 | register a set of ignite event-handlers to a specified ignite engine. args: engine: ignite engine, it can be a trainer, | STRING |
| HIGH | monai/handlers/mlflow_handler.py | 0 | register a set of ignite event-handlers to a specified ignite engine. args: engine: ignite engine, it can be a trainer, | STRING |
| HIGH | monai/handlers/stats_handler.py | 0 | register a set of ignite event-handlers to a specified ignite engine. args: engine: ignite engine, it can be a trainer, | STRING |
| HIGH | monai/handlers/tensorboard_handlers.py | 0 | handler for train or validation/evaluation epoch completed event. print epoch level log, default values are from ignite | STRING |
| HIGH | monai/handlers/mlflow_handler.py | 0 | handler for train or validation/evaluation epoch completed event. print epoch level log, default values are from ignite | STRING |
| HIGH | monai/handlers/stats_handler.py | 0 | handler for train or validation/evaluation epoch completed event. print epoch level log, default values are from ignite | STRING |
| HIGH | tests/metrics/test_hausdorff_distance.py | 0 | return a 3d image with a sphere inside. voxel values will be 1 inside the sphere, and 0 elsewhere. args: radius: radius | STRING |
| HIGH | tests/metrics/test_surface_distance.py | 0 | return a 3d image with a sphere inside. voxel values will be 1 inside the sphere, and 0 elsewhere. args: radius: radius | STRING |
| HIGH | tests/handlers/test_handler_hausdorff_distance.py | 0 | return a 3d image with a sphere inside. voxel values will be 1 inside the sphere, and 0 elsewhere. args: radius: radius | STRING |
| HIGH | tests/handlers/test_handler_surface_distance.py | 0 | return a 3d image with a sphere inside. voxel values will be 1 inside the sphere, and 0 elsewhere. args: radius: radius | STRING |
| HIGH | tests/losses/test_generalized_wasserstein_dice_loss.py | 0 | the goal of this test is to assess if the gradient of the loss function is correct by testing if we can train a one laye | STRING |
| HIGH | tests/integration/test_reg_loss_integration.py | 0 | the goal of this test is to assess if the gradient of the loss function is correct by testing if we can train a one laye | STRING |
| HIGH | tests/integration/test_seg_loss_integration.py | 0 | the goal of this test is to assess if the gradient of the loss function is correct by testing if we can train a one laye | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | monai/__init__.py | 106 | __all__ = [ | CODE |
| LOW | monai/metrics/wrapper.py | 28 | __all__ = ["MetricsReloadedBinary", "MetricsReloadedCategorical"] | CODE |
| LOW | monai/metrics/meandice.py | 27 | __all__ = ["DiceMetric", "compute_dice", "DiceHelper"] | CODE |
| LOW | monai/metrics/absolute_volume_difference.py | 21 | __all__ = ["AbsoluteVolumeDifferenceMetric", "compute_absolute_volume_difference"] | CODE |
| LOW | monai/metrics/embedding_collapse.py | 25 | __all__ = ["EmbeddingCollapseMetric", "compute_embedding_collapse"] | CODE |
| LOW | monai/metrics/panoptic_quality.py | 24 | __all__ = ["PanopticQualityMetric", "compute_panoptic_quality", "compute_mean_iou"] | CODE |
| LOW | monai/metrics/metric.py | 23 | __all__ = ["Metric", "IterationMetric", "Cumulative", "CumulativeIterationMetric"] | CODE |
| LOW | monai/metrics/utils.py | 48 | __all__ = [ | CODE |
| LOW | monai/metrics/hausdorff_distance.py | 31 | __all__ = ["HausdorffDistanceMetric", "compute_hausdorff_distance"] | CODE |
| LOW | monai/metrics/calibration.py | 23 | __all__ = ["CalibrationErrorMetric", "CalibrationReduction", "calibration_binning"] | CODE |
| LOW | monai/losses/spatial_mask.py | 22 | __all__ = ["MaskedLoss"] | CODE |
| LOW | monai/losses/boundary_loss.py | 24 | __all__ = ["BoundaryLoss"] | CODE |
| LOW | monai/losses/calibration.py | 23 | __all__ = ["HardL1ACELoss", "SoftL1ACELoss"] | CODE |
| LOW | monai/auto3dseg/analyzer.py | 44 | __all__ = [ | CODE |
| LOW | monai/auto3dseg/analyzer.py | 77 | def update_ops(self, key: str, op: Operations) -> None: | CODE |
| LOW | monai/auto3dseg/analyzer.py | 94 | def update_ops_nested_label(self, nested_key: str, op: Operations) -> None: | CODE |
| LOW | monai/auto3dseg/seg_summarizer.py | 31 | __all__ = ["SegSummarizer"] | CODE |
| LOW | monai/auto3dseg/operations.py | 20 | __all__ = ["Operations", "SampleOperations", "SummaryOperations"] | CODE |
| LOW | monai/auto3dseg/utils.py | 39 | __all__ = [ | CODE |
| LOW | monai/config/deviceconfig.py | 39 | __all__ = [ | CODE |
| LOW | monai/config/type_definitions.py | 36 | __all__ = [ | CODE |
| LOW | monai/bundle/config_parser.py | 34 | __all__ = ["ConfigParser"] | CODE |
| LOW | monai/bundle/config_item.py | 27 | __all__ = ["ComponentLocator", "ConfigItem", "ConfigExpression", "ConfigComponent", "Instantiable"] | CODE |
| LOW | monai/bundle/config_item.py | 142 | def update_config(self, config: Any) -> None: | CODE |
| LOW | monai/bundle/utils.py | 24 | __all__ = [ | CODE |
| LOW | monai/bundle/workflows.py | 37 | __all__ = ["BundleWorkflow", "ConfigWorkflow"] | CODE |
| LOW | monai/bundle/workflows.py | 784 | def _set_property(self, name: str, property: dict, value: Any) -> None: | CODE |
| LOW | monai/bundle/reference_resolver.py | 23 | __all__ = ["ReferenceResolver"] | CODE |
| LOW | monai/utils/safeeval.py | 20 | __all__ = ["SAFE_TYPES", "safe_eval"] | CODE |
| LOW | monai/utils/misc.py | 43 | __all__ = [ | CODE |
| LOW | monai/utils/enums.py | 20 | __all__ = [ | CODE |
| LOW | monai/utils/tf32.py | 18 | __all__ = ["has_ampere_or_later", "detect_default_tf32"] | CODE |
| LOW | monai/utils/type_conversion.py | 28 | __all__ = [ | CODE |
| LOW | monai/utils/deprecate_utils.py | 25 | __all__ = ["deprecated", "deprecated_arg", "DeprecatedError", "deprecated_arg_default"] | CODE |
| LOW | monai/utils/state_cacher.py | 27 | __all__ = ["StateCacher"] | CODE |
| LOW | monai/utils/module.py | 43 | __all__ = [ | CODE |
| LOW | monai/utils/nvtx.py | 30 | __all__ = ["Range"] | CODE |
| LOW | monai/utils/dist.py | 27 | __all__ = ["get_dist_device", "evenly_divisible_all_gather", "string_list_all_gather", "RankFilter"] | CODE |
| LOW | monai/utils/profiling.py | 40 | __all__ = [ | CODE |
| LOW | monai/utils/decorators.py | 16 | __all__ = ["RestartGenerator", "MethodReplacer"] | CODE |
| LOW | monai/visualize/class_activation_maps.py | 28 | __all__ = ["CAM", "GradCAM", "GradCAMpp", "ModelWithHooks", "default_normalizer"] | CODE |
| LOW | monai/visualize/gradient_based.py | 26 | __all__ = ["VanillaGrad", "SmoothGrad", "GuidedBackpropGrad", "GuidedBackpropSmoothGrad"] | CODE |
| LOW | monai/visualize/img2tensorboard.py | 39 | __all__ = ["make_animated_gif_summary", "add_animated_gif", "plot_2d_or_3d_image"] | CODE |
| LOW | monai/visualize/utils.py | 31 | __all__ = ["matshow3d", "blend_images"] | CODE |
| LOW | monai/visualize/visualizer.py | 21 | __all__ = ["default_upsampler"] | CODE |
| LOW | monai/optimizers/lr_scheduler.py | 19 | __all__ = ["LinearLR", "ExponentialLR"] | CODE |
| LOW | monai/optimizers/lr_finder.py | 43 | __all__ = ["LearningRateFinder"] | CODE |
| LOW | monai/optimizers/lr_finder.py | 378 | def _set_learning_rate(self, new_lrs: float | list) -> None: | CODE |
| LOW | monai/optimizers/utils.py | 20 | __all__ = ["generate_param_groups"] | CODE |
| LOW | monai/inferers/splitter.py | 28 | __all__ = ["Splitter", "SlidingWindowSplitter", "WSISlidingWindowSplitter"] | CODE |
| LOW | monai/inferers/splitter.py | 356 | def _set_reader(self, reader: str | BaseWSIReader | type[BaseWSIReader] | None, reader_kwargs: dict) -> None: | CODE |
| LOW | monai/inferers/utils.py | 39 | __all__ = ["sliding_window_inference"] | CODE |
| LOW | monai/inferers/inferer.py | 52 | __all__ = [ | CODE |
| LOW | monai/inferers/merger.py | 38 | __all__ = ["Merger", "AvgMerger", "ZarrAvgMerger"] | CODE |
| LOW | monai/networks/utils.py | 40 | __all__ = [ | CODE |
| LOW | monai/networks/blocks/cablock.py | 24 | __all__ = ["FeedForward", "CABlock"] | CODE |
| LOW | monai/networks/blocks/downsample.py | 23 | __all__ = ["MaxAvgPool", "DownSample", "Downsample", "SubpixelDownsample", "SubpixelDownSample", "Subpixeldownsample"] | CODE |
| LOW | monai/networks/blocks/pos_embed_utils.py | 20 | __all__ = ["build_fourier_position_embedding", "build_sincos_position_embedding"] | CODE |
| LOW | monai/networks/blocks/crf.py | 20 | __all__ = ["CRF"] | CODE |
| LOW | monai/networks/blocks/dints_block.py | 19 | __all__ = ["FactorizedIncreaseBlock", "FactorizedReduceBlock", "P3DActiConvNormBlock", "ActiConvNormBlock"] | CODE |
| 182 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | setup.py | 89 | CODE | |
| LOW | versioneer.py | 1195 | CODE | |
| LOW | versioneer.py | 1428 | CODE | |
| LOW | versioneer.py | 1753 | CODE | |
| LOW | versioneer.py | 2173 | CODE | |
| LOW | monai/_version.py | 157 | CODE | |
| LOW | monai/_version.py | 604 | CODE | |
| LOW | monai/metrics/utils.py | 135 | CODE | |
| LOW | monai/metrics/utils.py | 307 | CODE | |
| LOW | monai/metrics/surface_dice.py | 151 | CODE | |
| LOW | monai/metrics/confusion_matrix.py | 220 | CODE | |
| LOW | monai/losses/adversarial_loss.py | 50 | CODE | |
| LOW | monai/losses/ds_loss.py | 43 | CODE | |
| LOW | monai/losses/dice.py | 137 | CODE | |
| LOW | monai/losses/tversky.py | 112 | CODE | |
| LOW | monai/losses/focal_loss.py | 136 | CODE | |
| LOW | monai/auto3dseg/analyzer.py | 1007 | CODE | |
| LOW | monai/auto3dseg/utils.py | 185 | CODE | |
| LOW | monai/auto3dseg/utils.py | 269 | CODE | |
| LOW | monai/auto3dseg/utils.py | 398 | CODE | |
| LOW | monai/fl/client/monai_algo.py | 98 | CODE | |
| LOW | monai/fl/client/monai_algo.py | 334 | CODE | |
| LOW | monai/bundle/config_item.py | 73 | CODE | |
| LOW | monai/bundle/utils.py | 171 | CODE | |
| LOW | monai/bundle/utils.py | 241 | CODE | |
| LOW | monai/bundle/workflows.py | 274 | CODE | |
| LOW | monai/bundle/workflows.py | 529 | CODE | |
| LOW | monai/bundle/workflows.py | 820 | CODE | |
| LOW | monai/bundle/workflows.py | 852 | CODE | |
| LOW | monai/bundle/scripts.py | 142 | CODE | |
| LOW | monai/bundle/scripts.py | 410 | CODE | |
| LOW | monai/bundle/scripts.py | 449 | CODE | |
| LOW | monai/bundle/scripts.py | 782 | CODE | |
| LOW | monai/bundle/reference_resolver.py | 107 | CODE | |
| LOW | monai/bundle/reference_resolver.py | 283 | CODE | |
| LOW | monai/utils/misc.py | 395 | CODE | |
| LOW | monai/utils/misc.py | 496 | CODE | |
| LOW | monai/utils/jupyter_utils.py | 158 | CODE | |
| LOW | monai/utils/jupyter_utils.py | 305 | CODE | |
| LOW | monai/utils/type_conversion.py | 113 | CODE | |
| LOW | monai/utils/type_conversion.py | 196 | CODE | |
| LOW | monai/utils/type_conversion.py | 241 | CODE | |
| LOW | monai/utils/type_conversion.py | 286 | CODE | |
| LOW | monai/utils/type_conversion.py | 441 | CODE | |
| LOW | monai/utils/type_conversion.py | 452 | CODE | |
| LOW | monai/utils/ordering.py | 112 | CODE | |
| LOW | monai/utils/ordering.py | 158 | CODE | |
| LOW | monai/utils/ordering.py | 174 | CODE | |
| LOW | monai/utils/ordering.py | 193 | CODE | |
| LOW | monai/utils/module.py | 174 | CODE | |
| LOW | monai/utils/nvtx.py | 144 | CODE | |
| LOW | monai/utils/profiling.py | 240 | CODE | |
| LOW | monai/visualize/img2tensorboard.py | 146 | CODE | |
| LOW | monai/optimizers/novograd.py | 73 | CODE | |
| LOW | monai/inferers/utils.py | 42 | CODE | |
| LOW | monai/inferers/inferer.py | 310 | CODE | |
| LOW | monai/inferers/inferer.py | 619 | CODE | |
| LOW | monai/inferers/inferer.py | 915 | CODE | |
| LOW | monai/inferers/inferer.py | 1096 | CODE | |
| LOW | monai/inferers/inferer.py | 1706 | CODE | |
| 183 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | setup.py | 121 | except ValueError: | CODE |
| HIGH | versioneer.py | 389 | except NameError: | CODE |
| HIGH | versioneer.py | 1217 | except OSError: | CODE |
| HIGH | versioneer.py | 1457 | except OSError: | CODE |
| HIGH | versioneer.py | 1838 | except NotThisMethod: | CODE |
| HIGH | versioneer.py | 1858 | except NotThisMethod: | CODE |
| HIGH | versioneer.py | 1830 | except NotThisMethod: | CODE |
| HIGH | versioneer.py | 1849 | except NotThisMethod: | CODE |
| HIGH | monai/_version.py | 179 | except OSError: | CODE |
| HIGH | monai/_version.py | 653 | except NotThisMethod: | CODE |
| HIGH | monai/_version.py | 672 | except NotThisMethod: | CODE |
| HIGH | monai/_version.py | 678 | except NotThisMethod: | CODE |
| HIGH | monai/bundle/config_parser.py | 164 | except KeyError: | CODE |
| HIGH | monai/bundle/config_item.py | 92 | except ModuleNotFoundError: | CODE |
| HIGH | monai/utils/misc.py | 704 | except PermissionError: # project-monai/monai issue #3613 | CODE |
| HIGH | monai/utils/misc.py | 519 | except Exception: | CODE |
| HIGH | monai/utils/tf32.py | 44 | except Exception: | CODE |
| HIGH | monai/utils/module.py | 194 | except OptionalImportError: | CODE |
| HIGH | monai/utils/compare_sources.py | 38 | except TypeError: | CODE |
| HIGH | monai/utils/profiling.py | 229 | except Empty: | CODE |
| HIGH | monai/engines/workflow.py | 140 | except TypeError: # raised when data_loader has an iterable dataset with no length, or is some other type | CODE |
| HIGH | monai/data/dataset.py | 426 | except PermissionError: # project-monai/monai issue #3613 | CODE |
| HIGH | monai/data/dataset.py | 1710 | except PermissionError: # project-monai/monai issue #3613 | CODE |
| HIGH | monai/data/dataset.py | 424 | except FileExistsError: | CODE |
| HIGH | monai/data/dataset.py | 1708 | except FileExistsError: | CODE |
| HIGH | monai/data/image_reader.py | 1060 | except Exception: | CODE |
| HIGH | monai/data/thread_buffer.py | 53 | except Full: | CODE |
| HIGH | monai/data/thread_buffer.py | 77 | except Empty: | CODE |
| HIGH | monai/apps/utils.py | 284 | except (PermissionError, NotADirectoryError): # project-monai/monai issue #3613 #3757 for windows | CODE |
| HIGH | monai/apps/auto3dseg/auto_runner.py | 306 | except shutil.SameFileError: | CODE |
| HIGH | monai/apps/auto3dseg/utils.py | 62 | except Exception: | CODE |
| HIGH | monai/apps/detection/metrics/coco.py | 544 | except Exception: | CODE |
| HIGH | tests/test_utils.py | 217 | except Exception: | CODE |
| HIGH | tests/test_utils.py | 667 | except queue.Empty: # no result returned, took too long | CODE |
| HIGH | tests/integration/test_integration_workflows.py | 346 | except Exception: | CODE |
| HIGH | tests/fl/monai_algo/test_fl_monai_algo.py | 202 | except Exception: | CODE |
| HIGH | tests/networks/nets/test_resnet.py | 252 | except Exception: | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | runtests.sh | 1 | #! /bin/bash | COMMENT |
| LOW | .readthedocs.yml | 1 | # .readthedocs.yml | COMMENT |
| LOW | versioneer.py | 1881 | del sys.modules["versioneer"] | COMMENT |
| LOW | versioneer.py | 1921 | # we override "build_py" in setuptools | COMMENT |
| LOW | monai/metrics/hausdorff_distance.py | 281 | # arrives here as an all-infinite tensor. `torch.quantile` interpolates linearly | COMMENT |
| LOW | monai/losses/image_dissimilarity.py | 281 | COMMENT | |
| LOW | monai/losses/hausdorff_loss.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/csrc/resample/bounds_common.h | 21 | // It also defines an enumerated types that encodes each boundary type. | COMMENT |
| LOW | monai/csrc/resample/interpolation_common.h | 21 | // The entry points are: | COMMENT |
| LOW | monai/csrc/resample/pushpull_cpu.cpp | 21 | // Isotropic 0-th and 1-st order interpolation have their own (faster) | COMMENT |
| LOW | monai/csrc/resample/pushpull_cpu.cpp | 41 | #include <limits> | COMMENT |
| LOW | monai/csrc/resample/pushpull_cpu.cpp | 81 | COMMENT | |
| LOW | monai/csrc/resample/pushpull_cpu.cpp | 561 | // printf("do_grad: %d\n", do_grad); | COMMENT |
| LOW | monai/csrc/resample/pushpull_cpu.cpp | 721 | // This bit loops over all target voxels. We therefore need to | COMMENT |
| LOW | monai/csrc/utils/meta_macros.h | 21 | #define _DO_5(TARGET) TARGET(5) _DO_4(TARGET) | COMMENT |
| LOW | monai/csrc/utils/meta_macros.h | 41 | #define _DO_25(TARGET) TARGET(25) _DO_24(TARGET) | COMMENT |
| LOW | monai/csrc/utils/meta_macros.h | 61 | #define _DO_A_12(TARGET, A) TARGET(A, 12) _DO_A_11(TARGET, A) | COMMENT |
| LOW | monai/csrc/utils/meta_macros.h | 81 | #define _DO_A_32(TARGET, A) TARGET(A, 32) _DO_A_31(TARGET, A) | COMMENT |
| LOW | monai/csrc/utils/meta_macros.h | 101 | #define _DO_19_B(TARGET, B_RANGE) _DO_A_##B_RANGE(TARGET, 19) _DO_18_B(TARGET, B_RANGE) | COMMENT |
| LOW | monai/csrc/utils/resample_utils.h | 21 | // Note that if AT_PARALLEL_OPENMP = 1 but compilation does not use | COMMENT |
| LOW | monai/csrc/utils/resample_utils.h | 41 | #define MONAI_HOST __host__ | COMMENT |
| LOW | monai/config/type_definitions.py | 21 | # Commonly used concepts | COMMENT |
| LOW | monai/config/type_definitions.py | 41 | "NdarrayOrTensor", | COMMENT |
| LOW | monai/config/check_env.py | 1 | #! /usr/bin/env python | COMMENT |
| LOW | monai/config/__main__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/fl/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/fl/utils/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/fl/client/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/optimizers/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/blocks/mednext_block.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/blocks/backbone_fpn_utils.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/blocks/backbone_fpn_utils.py | 21 | COMMENT | |
| LOW | monai/networks/blocks/feature_pyramid_network.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/blocks/feature_pyramid_network.py | 21 | COMMENT | |
| LOW | monai/networks/nets/diffusion_model_unet.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/nets/hovernet.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/nets/mednext.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/nets/controlnet.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/nets/dynunet.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/nets/spade_diffusion_model_unet.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/schedulers/ddim.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/schedulers/ddim.py | 161 | pred_original_sample: Predicted original sample | COMMENT |
| LOW | monai/networks/schedulers/pndm.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/schedulers/pndm.py | 281 | # this function computes x_(t−δ) using the formula of (9) | COMMENT |
| LOW | monai/networks/schedulers/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/schedulers/rectified_flow.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/schedulers/scheduler.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/networks/schedulers/ddpm.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/_extensions/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/transforms/post/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/transforms/smooth_field/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/transforms/regularization/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/transforms/intensity/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/transforms/io/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/transforms/croppad/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/transforms/lazy/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/transforms/spatial/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/transforms/meta_utility/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/transforms/signal/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| LOW | monai/transforms/utility/__init__.py | 1 | # Copyright (c) MONAI Consortium | COMMENT |
| 120 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | versioneer.py | 515 | # This file is released into the public domain. | COMMENT |
| MEDIUM | monai/_version.py | 8 | # This file is released into the public domain. | COMMENT |
| MEDIUM | monai/config/type_definitions.py | 22 | # This module provides naming and type specifications for commonly used concepts | COMMENT |
| MEDIUM | monai/utils/nvtx.py | 79 | # Define the name to be associated to the range if not provided | COMMENT |
| MEDIUM | monai/utils/nvtx.py | 92 | # Define the methods to be wrapped if not provided | COMMENT |
| MEDIUM | monai/optimizers/lr_finder.py | 331 | # Create an iterator to get data batch by batch | COMMENT |
| MEDIUM | monai/optimizers/lr_finder.py | 517 | # Create the figure and axes object if axes was not already given | COMMENT |
| MEDIUM | monai/networks/nets/mednext.py | 268 | # Define the MedNeXt variants as reported in 10.48550/arXiv.2303.09975 | COMMENT |
| MEDIUM | monai/transforms/utils_morphological_ops.py | 110 | # Define the structuring element | COMMENT |
| MEDIUM | monai/data/wsi_datasets.py | 89 | # Create a default level that override all levels if it is not None | COMMENT |
| MEDIUM⚡ | monai/data/wsi_reader.py | 424 | # Create a list of patches and metadata | COMMENT |
| MEDIUM | monai/apps/reconstruction/transforms/array.py | 163 | # Create the mask | COMMENT |
| MEDIUM | monai/apps/reconstruction/transforms/array.py | 252 | # Create the mask | COMMENT |
| MEDIUM | tests/metrics/test_calibration_metric.py | 329 | # Create a 2-channel tensor where one channel has valid data and one is out of range | COMMENT |
| MEDIUM | tests/losses/test_generalized_wasserstein_dice_loss.py | 231 | # Create a batch of size 2 by repeating the same sample | COMMENT |
| MEDIUM | tests/losses/test_focal_loss.py | 104 | # Create a random tensor of shape (batch_size, class_num, 8, 4) | COMMENT |
| MEDIUM | tests/losses/test_focal_loss.py | 106 | # Create a random batch of classes | COMMENT |
| MEDIUM | tests/losses/test_focal_loss.py | 128 | # Create a random tensor of shape (batch_size, class_num, 8, 4) | COMMENT |
| MEDIUM | tests/losses/test_focal_loss.py | 130 | # Create a random batch of classes | COMMENT |
| MEDIUM | tests/losses/test_focal_loss.py | 152 | # Create a random tensor of shape (batch_size, class_num, 8, 4) | COMMENT |
| MEDIUM | tests/losses/test_focal_loss.py | 154 | # Create a random batch of classes | COMMENT |
| MEDIUM⚡ | tests/losses/test_focal_loss.py | 175 | # Create a random scores tensor of shape (batch_size, class_num) | COMMENT |
| MEDIUM⚡ | tests/losses/test_focal_loss.py | 177 | # Create a random batch of classes | COMMENT |
| MEDIUM | tests/losses/test_focal_loss.py | 199 | # Create a random scores tensor of shape (batch_size, class_num) | COMMENT |
| MEDIUM | tests/losses/test_focal_loss.py | 201 | # Create a random batch of classes | COMMENT |
| MEDIUM | tests/networks/layers/test_affine_transform.py | 391 | # Create a simple test image | COMMENT |
| MEDIUM⚡ | tests/transforms/test_nvtx_decorator.py | 220 | # Create a network | COMMENT |
| MEDIUM | tests/transforms/test_nvtx_decorator.py | 247 | # Create a network and loss | COMMENT |
| MEDIUM | tests/transforms/inverse/test_invertd.py | 310 | # Create a preprocessing pipeline | COMMENT |
| MEDIUM | tests/apps/test_download_and_extract.py | 98 | # Create a valid zip file | COMMENT |
| MEDIUM | tests/apps/test_download_and_extract.py | 148 | # Create a valid tar file | COMMENT |
| MEDIUM⚡ | tests/apps/test_download_and_extract.py | 189 | # Create a temporary file | COMMENT |
| MEDIUM | tests/apps/deepedit/test_deepedit_transforms.py | 288 | # Create a label array with different label values | COMMENT |
| MEDIUM⚡ | tests/handlers/test_handler_nvtx.py | 50 | # Define a range using one prefix (between BATCH_STARTED and BATCH_COMPLETED) | COMMENT |
| MEDIUM⚡ | tests/handlers/test_handler_nvtx.py | 52 | # Define a range using a pair of events | COMMENT |
| MEDIUM⚡ | tests/handlers/test_handler_nvtx.py | 54 | # Define a range using a pair of literals | COMMENT |
| MEDIUM⚡ | tests/handlers/test_handler_nvtx.py | 56 | # Define a range using a pair of literal and events | COMMENT |
| MEDIUM⚡ | tests/handlers/test_handler_nvtx.py | 58 | # Define the start of range using literal | COMMENT |
| MEDIUM⚡ | tests/handlers/test_handler_nvtx.py | 60 | # Define the start of range using event | COMMENT |
| MEDIUM⚡ | tests/handlers/test_handler_nvtx.py | 62 | # Define the start of range using literals and providing message | COMMENT |
| MEDIUM⚡ | tests/handlers/test_handler_nvtx.py | 64 | # Define the end of range using Ignite Event | COMMENT |
| MEDIUM⚡ | tests/handlers/test_handler_nvtx.py | 67 | # Define the end of range using literal | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| CRITICAL | monai/networks/nets/swin_unetr.py | 356 | self.swinViT.patch_embed.proj.weight.copy_(wstate["module.patch_embed.proj.weight"]) | CODE |
| CRITICAL | monai/networks/nets/swin_unetr.py | 357 | self.swinViT.patch_embed.proj.bias.copy_(wstate["module.patch_embed.proj.bias"]) | CODE |
| CRITICAL | monai/apps/detection/networks/retinanet_detector.py | 114 | Input argument ``network`` can be a monai.apps.detection.networks.retinanet_network.RetinaNet(*) object, | STRING |
| CRITICAL | monai/apps/detection/networks/retinanet_detector.py | 171 | anchor_generator = monai.apps.detection.utils.anchor_utils.AnchorGeneratorWithAnchorShape( | STRING |
| CRITICAL | monai/apps/detection/networks/retinanet_detector.py | 1059 | anchor_generator = monai.apps.detection.utils.anchor_utils.AnchorGeneratorWithAnchorShape( | STRING |
| CRITICAL | tests/integration/test_integration_nnunetv2_runner.py | 33 | monai.apps.nnunet.nnunetv2_runner.logger.setLevel(logging.ERROR) # suppress warning logging to clean up test output | CODE |
| CRITICAL⚡ | tests/networks/blocks/test_CABlock.py | 121 | block.qkv.conv.weight.data.fill_(1.0) | CODE |
| CRITICAL⚡ | tests/networks/blocks/test_CABlock.py | 122 | block.qkv_dwconv.conv.weight.data.fill_(1.0) | CODE |
| CRITICAL⚡ | tests/networks/blocks/test_CABlock.py | 124 | block.project_out.conv.weight.data.fill_(1.0) | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | monai/__init__.py | 134 | except Exception: | CODE |
| LOW | monai/metrics/embedding_collapse.py | 393 | except Exception as exc: | CODE |
| LOW | monai/config/deviceconfig.py | 131 | except Exception: | CODE |
| MEDIUM | monai/config/deviceconfig.py | 128 | def _dict_append(in_dict, key, fn): | CODE |
| LOW | monai/config/check_env.py | 99 | except Exception as e: | STRING |
| LOW | monai/config/check_env.py | 137 | except Exception as e: | STRING |
| LOW | monai/fl/client/monai_algo.py | 72 | except Exception as e: | CODE |
| LOW | monai/bundle/config_item.py | 375 | except Exception as e: | CODE |
| LOW | monai/utils/misc.py | 154 | except Exception: | CODE |
| LOW | monai/utils/misc.py | 519 | except Exception: | CODE |
| LOW | monai/utils/tf32.py | 44 | except Exception: | CODE |
| LOW | monai/utils/tf32.py | 74 | except Exception: | CODE |
| LOW | monai/utils/module.py | 254 | except Exception as e: | CODE |
| LOW | monai/utils/module.py | 389 | except Exception as import_exception: # any exceptions during import | CODE |
| LOW | monai/inferers/utils.py | 229 | except Exception as e: | CODE |
| LOW | monai/inferers/inferer.py | 549 | except Exception as e: | CODE |
| LOW | monai/networks/trt_compiler.py | 101 | except Exception as e: | CODE |
| LOW | monai/networks/trt_compiler.py | 199 | except Exception: | CODE |
| LOW | monai/networks/trt_compiler.py | 425 | except Exception as e: | CODE |
| LOW | monai/networks/trt_compiler.py | 457 | except Exception as e: | CODE |
| LOW | monai/networks/trt_compiler.py | 491 | except Exception as e: | CODE |
| LOW | monai/networks/nets/resnet.py | 656 | except Exception: | CODE |
| LOW | monai/transforms/transform.py | 156 | except Exception as e: | CODE |
| LOW | monai/transforms/io/array.py | 292 | except Exception as e: | CODE |
| LOW | monai/transforms/io/array.py | 531 | except Exception as e: | CODE |
| LOW | monai/data/image_writer.py | 116 | except Exception: # other writer init errors indicating it exists | CODE |
| LOW | monai/data/dataset.py | 84 | except Exception as e: | CODE |
| LOW | monai/data/dataset.py | 704 | except Exception as err: | CODE |
| LOW | monai/data/image_reader.py | 1060 | except Exception: | CODE |
| LOW⚡ | monai/data/nvimgcodec_pydicom_plugin.py | 60 | except Exception as exc: # pragma: no cover - environment specific | CODE |
| LOW | monai/apps/utils.py | 192 | except Exception as e: | CODE |
| LOW | monai/apps/utils.py | 389 | except Exception as e: | CODE |
| LOW | monai/apps/auto3dseg/ensemble_builder.py | 219 | except Exception: | CODE |
| LOW | monai/apps/auto3dseg/bundle_gen.py | 432 | except Exception as e: | CODE |
| LOW | monai/apps/auto3dseg/utils.py | 62 | except Exception: | CODE |
| LOW | monai/apps/auto3dseg/data_analyzer.py | 344 | except Exception as err: | CODE |
| LOW | monai/apps/auto3dseg/data_analyzer.py | 360 | except Exception as err: | CODE |
| LOW | monai/apps/vista3d/transforms.py | 114 | except Exception: | CODE |
| LOW | monai/apps/detection/metrics/coco.py | 544 | except Exception: | CODE |
| LOW | monai/apps/nnunet/nnunetv2_runner.py | 248 | except Exception: | CODE |
| LOW | monai/apps/nnunet/nnunetv2_runner.py | 327 | except Exception as err: | CODE |
| LOW | monai/handlers/mlflow_handler.py | 380 | except Exception as e: | CODE |
| LOW | monai/handlers/mlflow_handler.py | 403 | except Exception as e: | CODE |
| LOW | tests/clang_format_utils.py | 66 | except Exception as e: | CODE |
| LOW | tests/test_utils.py | 217 | except Exception: | CODE |
| LOW | tests/test_utils.py | 353 | except Exception: | CODE |
| LOW | tests/test_utils.py | 541 | except Exception as e: | CODE |
| LOW | tests/test_utils.py | 625 | except Exception as e: | CODE |
| MEDIUM | tests/test_utils.py | 621 | def run_process(func, args, kwargs, results): | CODE |
| LOW | tests/runner.py | 192 | except Exception: | CODE |
| LOW | tests/integration/test_integration_workflows.py | 341 | except Exception as e: | CODE |
| LOW | tests/integration/test_integration_workflows.py | 346 | except Exception: | CODE |
| LOW | tests/fl/monai_algo/test_fl_monai_algo.py | 202 | except Exception: | CODE |
| LOW | tests/networks/nets/test_resnet.py | 252 | except Exception: | CODE |
| LOW | tests/networks/nets/test_dynunet.py | 153 | except Exception: | CODE |
| MEDIUM | tests/networks/nets/test_dynunet.py | 147 | def setUp(self): | CODE |
| LOW | tests/transforms/test_rand_simulate_low_resolution.py | 115 | except Exception as e: | CODE |
| LOW | tests/data/test_nvimgcodec_pydicom_reader.py | 269 | except Exception as error: | CODE |
| LOW | tests/apps/test_download_and_extract.py | 122 | except Exception as e: | CODE |
| LOW⚡ | tests/apps/test_download_and_extract.py | 176 | except Exception as e: | CODE |
| 6 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | monai/auto3dseg/utils.py | 482 | # Check if this is a legacy pickle file | COMMENT |
| LOW | monai/bundle/scripts.py | 357 | # Check if the data is a dictionary and it has the key 'modelVersions' | COMMENT |
| LOW | monai/utils/nvtx.py | 98 | # Check if to append method's name to the range's name | COMMENT |
| LOW | monai/optimizers/lr_finder.py | 225 | # Check if the optimizer is already attached to a scheduler | COMMENT |
| LOW | monai/optimizers/lr_finder.py | 308 | # Check if the optimizer is already attached to a scheduler | COMMENT |
| LOW | monai/optimizers/lr_finder.py | 366 | # Check if the loss has diverged; if it has, stop the test | COMMENT |
| LOW | monai/optimizers/lr_finder.py | 432 | # Set model to evaluation mode and disable gradient computation | COMMENT |
| LOW | monai/inferers/splitter.py | 413 | # Check if the input is a sting or path like | COMMENT |
| LOW | monai/inferers/inferer.py | 791 | # Check if ``roi_size`` tuple is 2D and ``inputs`` tensor is 3D | COMMENT |
| LOW | monai/transforms/utils.py | 1801 | # Set all to True | COMMENT |
| LOW⚡ | monai/data/wsi_reader.py | 410 | # Check if there are four color channels for RGBA | COMMENT |
| LOW⚡ | monai/data/wsi_reader.py | 417 | # Check if there are three color channels for RGB | COMMENT |
| LOW | monai/data/wsi_reader.py | 488 | # Check if user-provided mpp_x and mpp_y fall within the tolerance intervals for closest level | COMMENT |
| LOW | monai/data/wsi_reader.py | 982 | # Check if the color channel is 3 (RGB) or 4 (RGBA) | COMMENT |
| LOW | monai/data/wsi_reader.py | 1532 | # Check if the color channel is 3 (RGB) or 4 (RGBA) | COMMENT |
| LOW | monai/apps/detection/transforms/dictionary.py | 617 | # Check if random transform was actually performed (based on `prob`) | COMMENT |
| LOW | monai/apps/detection/transforms/dictionary.py | 762 | # Check if random transform was actually performed (based on `prob`) | COMMENT |
| LOW | monai/apps/detection/transforms/dictionary.py | 1380 | # Check if random transform was actually performed (based on `prob`) | COMMENT |
| LOW | …/apps/generation/maisi/networks/autoencoderkl_maisi.py | 560 | # Check if attention_levels and num_channels have the same size | COMMENT |
| LOW | …/apps/generation/maisi/networks/autoencoderkl_maisi.py | 564 | # Check if num_res_blocks and num_channels have the same size | COMMENT |
| LOW | tests/bundle/test_bundle_workflow.py | 422 | # Close the file handler `fileConfig` attached to the root logger before the tempdir is | COMMENT |
| LOW | tests/transforms/test_nvtx_transform.py | 63 | # Check if chain of randomizable/non-randomizable transforms is not broken | COMMENT |
| LOW⚡ | tests/transforms/test_nvtx_decorator.py | 203 | # Check if the outputs are equal | COMMENT |
| LOW⚡ | tests/transforms/test_nvtx_decorator.py | 212 | # Check if the first randomized is RandAdjustContrast | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | versioneer.py | 534 | # each be defined on a line of their own. _version.py will just call | COMMENT |
| LOW | monai/_version.py | 27 | # each be defined on a line of their own. _version.py will just call | COMMENT |
| MEDIUM | monai/data/dataset.py | 409 | # to make the cache more robust to manual killing of parent process | COMMENT |
| MEDIUM | monai/data/dataset.py | 1691 | # to make the cache more robust to manual killing of parent process | COMMENT |
| MEDIUM | tests/handlers/test_handler_stats.py | 262 | # leverage `engine.logger` to print info | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tests/integration/test_auto3dseg_ensemble.py | 132 | "name": "fake_data", | CODE |
| LOW | tests/integration/test_auto3dseg_hpo.py | 112 | "name": "fake_data", | CODE |
| LOW | tests/integration/test_integration_gpu_customization.py | 105 | "name": "fake_data", | CODE |
| LOW | tests/bundle/test_config_parser.py | 179 | parser.set("fake_key", "transform#other_transforms#keys", True) | CODE |
| LOW | tests/bundle/test_config_parser.py | 180 | self.assertEqual(parser.get(id="transform#other_transforms#keys"), "fake_key") | CODE |
| LOW | tests/apps/test_auto3dseg_bundlegen.py | 112 | "name": "fake_data", | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | monai/transforms/post/array.py | 414 | # If the affine of the data is not identity, you can also add Spacing before. | STRING |
| MEDIUM | monai/apps/pathology/handlers/utils.py | 31 | Here is a simple example:: | STRING |
| MEDIUM | .github/workflows/codeql-analysis.yml | 64 | # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW⚡ | tests/transforms/test_spatial_cropd.py | 189 | # Step 1: convert world -> image coordinates | COMMENT |
| LOW⚡ | tests/transforms/test_spatial_cropd.py | 195 | # Step 2: crop using string keys | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW⚡ | tests/transforms/test_spatial_cropd.py | 189 | # Step 1: convert world -> image coordinates | COMMENT |
| LOW⚡ | tests/transforms/test_spatial_cropd.py | 195 | # Step 2: crop using string keys | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | monai/apps/utils.py | 217 | If undefined, `os.path.basename(url)` will be used. | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | tests/bundle/test_config_parser.py | 198 | def test_function(self, config): | CODE |
| LOW | tests/utils/test_require_pkg.py | 29 | def test_function(self): | CODE |