project_name string | class_name string | class_modifiers string | class_implements int64 | class_extends int64 | function_name string | function_body string | cyclomatic_complexity int64 | NLOC int64 | num_parameter int64 | num_token int64 | num_variable int64 | start_line int64 | end_line int64 | function_index int64 | function_params string | function_variable string | function_return_type string | function_body_line_type string | function_num_functions int64 | function_num_lines int64 | outgoing_function_count int64 | outgoing_function_names string | incoming_function_count int64 | incoming_function_names string | lexical_representation string |
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CAREamics_careamics | HyperParametersCallback | public | 0 | 1 | __init__ | def __init__(self, config: Configuration) -> None:"""Constructor.Parameters----------config : ConfigurationCAREamics configuration to be saved as hyperparameter in the model."""self.config = config | 1 | 2 | 2 | 17 | 0 | 27 | 36 | 27 | self,config | [] | None | {"Assign": 1, "Expr": 1} | 0 | 10 | 0 | [] | 8,182 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.15197461_googleapis_python_cloud_core.google.cloud._helpers.__init___py._LocalStack.__init__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16798231_kapji_capital_gains_calculator.cgt_calc.exceptions_py.AmountMissi... | The function (__init__) defined within the public class called HyperParametersCallback, that inherit another class.The function start at line 27 and ends at 36. It contains 2 lines of code and it has a cyclomatic complexity of 1. It takes 2 parameters, represented as [27.0] and does not return any value. It has 8182.0 ... |
CAREamics_careamics | HyperParametersCallback | public | 0 | 1 | on_train_start | def on_train_start(self, trainer: Trainer, pl_module: LightningModule) -> None:"""Update the hyperparameters of the model with the configuration on train start.Parameters----------trainer : TrainerPyTorch Lightning trainer, unused.pl_module : LightningModulePyTorch Lightning module."""pl_module.hparams.update(self.conf... | 1 | 2 | 3 | 30 | 0 | 38 | 49 | 38 | self,trainer,pl_module | [] | None | {"Expr": 2} | 2 | 12 | 2 | ["pl_module.hparams.update", "self.config.model_dump"] | 0 | [] | The function (on_train_start) defined within the public class called HyperParametersCallback, that inherit another class.The function start at line 38 and ends at 49. It contains 2 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [38.0] and does not return any value. It decla... |
CAREamics_careamics | ProgressBarCallback | public | 0 | 1 | init_train_tqdm | def init_train_tqdm(self) -> tqdm:"""Override this to customize the tqdm bar for training.Returns-------tqdmA tqdm bar."""bar = tqdm(desc="Training",position=(2 * self.process_position),disable=self.is_disabled,leave=True,dynamic_ncols=True,file=sys.stdout,smoothing=0,)return bar | 1 | 11 | 1 | 53 | 0 | 14 | 31 | 14 | self | [] | tqdm | {"Assign": 1, "Expr": 1, "Return": 1} | 1 | 18 | 1 | ["tqdm"] | 0 | [] | The function (init_train_tqdm) defined within the public class called ProgressBarCallback, that inherit another class.The function start at line 14 and ends at 31. It contains 11 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters and does not return any value. It declare 1.... |
CAREamics_careamics | ProgressBarCallback | public | 0 | 1 | init_validation_tqdm | def init_validation_tqdm(self) -> tqdm:"""Override this to customize the tqdm bar for validation.Returns-------tqdmA tqdm bar."""# The main progress bar doesn't exist in `trainer.validate()`has_main_bar = self.train_progress_bar is not Nonebar = tqdm(desc="Validating",position=(2 * self.process_position + has_main_bar)... | 1 | 11 | 1 | 59 | 0 | 33 | 51 | 33 | self | [] | tqdm | {"Assign": 2, "Expr": 1, "Return": 1} | 1 | 19 | 1 | ["tqdm"] | 0 | [] | The function (init_validation_tqdm) defined within the public class called ProgressBarCallback, that inherit another class.The function start at line 33 and ends at 51. It contains 11 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters and does not return any value. It decla... |
CAREamics_careamics | ProgressBarCallback | public | 0 | 1 | init_test_tqdm | def init_test_tqdm(self) -> tqdm:"""Override this to customize the tqdm bar for testing.Returns-------tqdmA tqdm bar."""bar = tqdm(desc="Testing",position=(2 * self.process_position),disable=self.is_disabled,leave=True,dynamic_ncols=False,ncols=100,file=sys.stdout,)return bar | 1 | 11 | 1 | 53 | 0 | 53 | 70 | 53 | self | [] | tqdm | {"Assign": 1, "Expr": 1, "Return": 1} | 1 | 18 | 1 | ["tqdm"] | 0 | [] | The function (init_test_tqdm) defined within the public class called ProgressBarCallback, that inherit another class.The function start at line 53 and ends at 70. It contains 11 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters and does not return any value. It declare 1.0... |
CAREamics_careamics | ProgressBarCallback | public | 0 | 1 | get_metrics | def get_metrics(self, trainer: Trainer, pl_module: LightningModule) -> dict[str, Union[int, str, float, dict[str, float]]]:"""Override this to customize the metrics displayed in the progress bar.Parameters----------trainer : TrainerThe trainer object.pl_module : LightningModuleThe LightningModule object, unused.Returns... | 1 | 5 | 3 | 45 | 0 | 72 | 90 | 72 | self,trainer,pl_module | [] | dict[str, Union[int, str, float, dict[str, float]]] | {"Assign": 1, "Expr": 1, "Return": 1} | 0 | 19 | 0 | [] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.3704533_opentsdb_tcollector.collectors.available.software.long_lived.mapr_metrics_py.Metrics2TSD.run"] | The function (get_metrics) defined within the public class called ProgressBarCallback, that inherit another class.The function start at line 72 and ends at 90. It contains 5 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [72.0] and does not return any value. It has 1.0 func... |
CAREamics_careamics | public | public | 0 | 0 | get_sample_file_path | def get_sample_file_path(dataset: Union[IterableTiledPredDataset, IterablePredDataset], sample_id: int) -> Path:"""Get the file path for a particular sample.Parameters----------dataset : IterableTiledPredDataset or IterablePredDatasetDataset.sample_id : intSample ID, the index of the file in the dataset `dataset`.Retur... | 1 | 4 | 2 | 26 | 0 | 10 | 28 | 10 | dataset,sample_id | [] | Path | {"Expr": 1, "Return": 1} | 0 | 19 | 0 | [] | 4 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lightning.callbacks.prediction_writer_callback.write_strategy_py.CacheTiles.write_batch", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.car... | The function (get_sample_file_path) defined within the public class called public.The function start at line 10 and ends at 28. It contains 4 lines of code and it has a cyclomatic complexity of 1. It takes 2 parameters, represented as [10.0] and does not return any value. It has 4.0 functions calling this function whic... |
CAREamics_careamics | public | public | 0 | 0 | create_write_file_path | def create_write_file_path(dirpath: Path, file_path: Path, write_extension: str) -> Path:"""Create the file name for the output file.Takes the original file path, changes the directory to `dirpath` and changesthe extension to `write_extension`.Parameters----------dirpath : pathlib.PathThe output directory to write file... | 1 | 6 | 3 | 38 | 2 | 31 | 56 | 31 | dirpath,file_path,write_extension | ['file_path', 'file_name'] | Path | {"Assign": 2, "Expr": 1, "Return": 1} | 2 | 26 | 2 | ["with_suffix", "Path"] | 3 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lightning.callbacks.prediction_writer_callback.write_strategy_py.CacheTiles.write_batch", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.car... | The function (create_write_file_path) defined within the public class called public.The function start at line 31 and ends at 56. It contains 6 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [31.0] and does not return any value. It declares 2.0 functions, It has 2.0 functio... |
CAREamics_careamics | PredictionWriterCallback | public | 0 | 1 | __init__ | def __init__(self,write_strategy: WriteStrategy,dirpath: Union[Path, str] = "predictions",):"""A PyTorch Lightning callback to save predictions.Parameters----------write_strategy : WriteStrategyA strategy for writing predictions.dirpath : pathlib.Path or str, default="predictions"The path to the directory where predict... | 1 | 10 | 3 | 57 | 0 | 53 | 80 | 53 | self,write_strategy,dirpath | [] | None | {"AnnAssign": 3, "Expr": 3} | 3 | 28 | 3 | ["__init__", "super", "self._init_dirpath"] | 8,182 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.15197461_googleapis_python_cloud_core.google.cloud._helpers.__init___py._LocalStack.__init__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16798231_kapji_capital_gains_calculator.cgt_calc.exceptions_py.AmountMissi... | The function (__init__) defined within the public class called PredictionWriterCallback, that inherit another class.The function start at line 53 and ends at 80. It contains 10 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [53.0] and does not return any value. It declares ... |
CAREamics_careamics | PredictionWriterCallback | public | 0 | 1 | from_write_func_params | def from_write_func_params(cls,write_type: SupportedWriteType,tiled: bool,write_func: WriteFunc | None = None,write_extension: str | None = None,write_func_kwargs: dict[str, Any] | None = None,dirpath: Union[Path, str] = "predictions",) -> PredictionWriterCallback:# TODO: change type hint to self (find out how)"""Initi... | 1 | 17 | 7 | 93 | 0 | 83 | 129 | 83 | cls,write_type,tiled,write_func,write_extension,write_func_kwargs,dirpath | [] | PredictionWriterCallback | {"Assign": 1, "Expr": 1, "Return": 1} | 2 | 47 | 2 | ["create_write_strategy", "cls"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.tests.lightning.callbacks.prediction_writer_callback.test_prediction_writer_callback_py.test_from_write_func_params"] | The function (from_write_func_params) defined within the public class called PredictionWriterCallback, that inherit another class.The function start at line 83 and ends at 129. It contains 17 lines of code and it has a cyclomatic complexity of 1. It takes 7 parameters, represented as [83.0] and does not return any valu... |
CAREamics_careamics | PredictionWriterCallback | public | 0 | 1 | _init_dirpath | def _init_dirpath(self, dirpath):"""Initialize directory path. Should only be called from `__init__`.Parameters----------dirpath : pathlib.PathSee `__init__` description."""dirpath = Path(dirpath)if not dirpath.is_absolute():dirpath = Path.cwd() / dirpathlogger.warning("Prediction output directory is not absolute, abso... | 2 | 9 | 2 | 44 | 0 | 131 | 147 | 131 | self,dirpath | [] | None | {"Assign": 3, "Expr": 2, "If": 1} | 4 | 17 | 4 | ["Path", "dirpath.is_absolute", "Path.cwd", "logger.warning"] | 0 | [] | The function (_init_dirpath) defined within the public class called PredictionWriterCallback, that inherit another class.The function start at line 131 and ends at 147. It contains 9 lines of code and it has a cyclomatic complexity of 2. It takes 2 parameters, represented as [131.0] and does not return any value. It de... |
CAREamics_careamics | PredictionWriterCallback | public | 0 | 1 | setup | def setup(self, trainer: Trainer, pl_module: LightningModule, stage: str) -> None:"""Create the prediction output directory when predict begins.Called when fit, validate, test, predict, or tune begins.Parameters----------trainer : TrainerPyTorch Lightning trainer.pl_module : LightningModulePyTorch Lightning module.stag... | 2 | 5 | 4 | 57 | 0 | 149 | 168 | 149 | self,trainer,pl_module,stage | [] | None | {"Expr": 4, "If": 1} | 4 | 20 | 4 | ["setup", "super", "logger.info", "self.dirpath.mkdir"] | 23 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16418165_szabgab_pydigger_com.PyDigger.fetch_py.main", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.3584344_influxgraph_influxgraph.setup_py.run_setup", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.... | The function (setup) defined within the public class called PredictionWriterCallback, that inherit another class.The function start at line 149 and ends at 168. It contains 5 lines of code and it has a cyclomatic complexity of 2. It takes 4 parameters, represented as [149.0] and does not return any value. It declares 4... |
CAREamics_careamics | PredictionWriterCallback | public | 0 | 1 | write_on_batch_end | def write_on_batch_end(self,trainer: Trainer,pl_module: LightningModule,prediction: Any,# TODO: change to expected typebatch_indices: Sequence[int] | None,batch: Any,# TODO: change to expected typebatch_idx: int,dataloader_idx: int,) -> None:"""Write predictions at the end of a batch.The method of prediction is determi... | 5 | 38 | 8 | 156 | 0 | 170 | 234 | 170 | self,trainer,pl_module,prediction,batch_indices,batch,batch_idx,dataloader_idx | [] | None | {"AnnAssign": 3, "Expr": 2, "If": 2, "Return": 1} | 5 | 65 | 5 | ["isinstance", "isinstance", "isinstance", "TypeError", "self.write_strategy.write_batch"] | 0 | [] | The function (write_on_batch_end) defined within the public class called PredictionWriterCallback, that inherit another class.The function start at line 170 and ends at 234. It contains 38 lines of code and it has a cyclomatic complexity of 5. It takes 8 parameters, represented as [170.0] and does not return any value.... |
CAREamics_careamics | WriteStrategy | public | 1 | 1 | write_batch | def write_batch(self,trainer: Trainer,pl_module: LightningModule,prediction: Any,# TODO: change to expected typebatch_indices: Sequence[int] | None,batch: Any,# TODO: change to expected typebatch_idx: int,dataloader_idx: int,dirpath: Path,) -> None:"""WriteStrategy subclasses must contain this function to write a batch... | 1 | 11 | 9 | 46 | 0 | 23 | 55 | 23 | self,trainer,pl_module,prediction,batch_indices,batch,batch_idx,dataloader_idx,dirpath | [] | None | {"Expr": 1} | 0 | 33 | 0 | [] | 0 | [] | The function (write_batch) defined within the public class called WriteStrategy, implement an interface, and it inherit another class.The function start at line 23 and ends at 55. It contains 11 lines of code and it has a cyclomatic complexity of 1. It takes 9 parameters, represented as [23.0] and does not return any v... |
CAREamics_careamics | CacheTiles | public | 0 | 1 | __init__ | def __init__(self,write_func: WriteFunc,write_extension: str,write_func_kwargs: dict[str, Any],) -> None:"""A write strategy that will cache tiles.Tiles are cached until a whole image is predicted on. Then the stitchedprediction is saved.Parameters----------write_func : WriteFuncFunction used to save predictions.write_... | 1 | 12 | 4 | 81 | 0 | 88 | 117 | 88 | self,write_func,write_extension,write_func_kwargs | [] | None | {"AnnAssign": 5, "Expr": 2} | 2 | 30 | 2 | ["__init__", "super"] | 8,182 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.15197461_googleapis_python_cloud_core.google.cloud._helpers.__init___py._LocalStack.__init__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16798231_kapji_capital_gains_calculator.cgt_calc.exceptions_py.AmountMissi... | The function (__init__) defined within the public class called CacheTiles, that inherit another class.The function start at line 88 and ends at 117. It contains 12 lines of code and it has a cyclomatic complexity of 1. It takes 4 parameters, represented as [88.0] and does not return any value. It declares 2.0 functions... |
CAREamics_careamics | CacheTiles | public | 0 | 1 | last_tiles | def last_tiles(self) -> list[bool]:"""List of bool to determine whether each tile in the cache is the last tile.Returns-------list of boolWhether each tile in the tile cache is the last tile."""return [tile_info.last_tile for tile_info in self.tile_info_cache] | 2 | 2 | 1 | 23 | 0 | 120 | 129 | 120 | self | [] | list[bool] | {"Expr": 1, "Return": 1} | 0 | 10 | 0 | [] | 0 | [] | The function (last_tiles) defined within the public class called CacheTiles, that inherit another class.The function start at line 120 and ends at 129. It contains 2 lines of code and it has a cyclomatic complexity of 2. The function does not take any parameters and does not return any value.. |
CAREamics_careamics | WriteStrategy | public | 1 | 1 | write_batch | def write_batch(self,trainer: Trainer,pl_module: LightningModule,prediction: tuple[NDArray, list[TileInformation]],batch_indices: Sequence[int] | None,batch: tuple[NDArray, list[TileInformation]],batch_idx: int,dataloader_idx: int,dirpath: Path,) -> None:"""Cache tiles until the last tile is predicted; save the stitche... | 4 | 38 | 9 | 246 | 0 | 131 | 200 | 131 | self,trainer,pl_module,prediction,batch_indices,batch,batch_idx,dataloader_idx,dirpath | [] | None | {"Expr": 1} | 0 | 33 | 0 | [] | 0 | [] | The function (write_batch) defined within the public class called WriteStrategy, implement an interface, and it inherit another class.The function start at line 131 and ends at 200. It contains 38 lines of code and it has a cyclomatic complexity of 4. It takes 9 parameters, represented as [131.0] and does not return an... |
CAREamics_careamics | CacheTiles | public | 0 | 1 | _has_last_tile | def _has_last_tile(self) -> bool:"""Whether a last tile is contained in the cached tiles.Returns-------boolWhether a last tile is contained in the cached tiles."""return any(self.last_tiles) | 1 | 2 | 1 | 15 | 0 | 202 | 211 | 202 | self | [] | bool | {"Expr": 1, "Return": 1} | 1 | 10 | 1 | ["any"] | 0 | [] | The function (_has_last_tile) defined within the public class called CacheTiles, that inherit another class.The function start at line 202 and ends at 211. It contains 2 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters and does not return any value. It declare 1.0 functio... |
CAREamics_careamics | CacheTiles | public | 0 | 1 | _clear_cache | def _clear_cache(self) -> None:"""Remove the tiles in the cache up to the first last tile."""index = self._last_tile_index()self.tile_cache = self.tile_cache[index + 1 :]self.tile_info_cache = self.tile_info_cache[index + 1 :] | 1 | 4 | 1 | 41 | 0 | 213 | 217 | 213 | self | [] | None | {"Assign": 3, "Expr": 1} | 1 | 5 | 1 | ["self._last_tile_index"] | 0 | [] | The function (_clear_cache) defined within the public class called CacheTiles, that inherit another class.The function start at line 213 and ends at 217. It contains 4 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters and does not return any value. It declare 1.0 function,... |
CAREamics_careamics | CacheTiles | public | 0 | 1 | _last_tile_index | def _last_tile_index(self) -> int:"""Find the index of the last tile in the tile cache.Returns-------intIndex of last tile.Raises------ValueErrorIf there is no last tile in the tile cache."""last_tiles = self.last_tilesif not any(last_tiles):raise ValueError("No last tile in the tile cache.")index = np.where(last_tiles... | 2 | 6 | 1 | 41 | 0 | 219 | 237 | 219 | self | [] | int | {"Assign": 2, "Expr": 1, "If": 1, "Return": 1} | 3 | 19 | 3 | ["any", "ValueError", "np.where"] | 0 | [] | The function (_last_tile_index) defined within the public class called CacheTiles, that inherit another class.The function start at line 219 and ends at 237. It contains 6 lines of code and it has a cyclomatic complexity of 2. The function does not take any parameters and does not return any value. It declares 3.0 func... |
CAREamics_careamics | CacheTiles | public | 0 | 1 | _get_image_tiles | def _get_image_tiles(self) -> tuple[list[NDArray], list[TileInformation]]:"""Get the tiles corresponding to a single image.Returns-------tuple of (list of numpy.ndarray, list of TileInformation)Tiles and tile information to stitch together a full image."""index = self._last_tile_index()tiles = self.tile_cache[: index +... | 1 | 5 | 1 | 52 | 0 | 239 | 251 | 239 | self | [] | tuple[list[NDArray], list[TileInformation]] | {"Assign": 3, "Expr": 1, "Return": 1} | 1 | 13 | 1 | ["self._last_tile_index"] | 0 | [] | The function (_get_image_tiles) defined within the public class called CacheTiles, that inherit another class.The function start at line 239 and ends at 251. It contains 5 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters and does not return any value. It declare 1.0 funct... |
CAREamics_careamics | WriteStrategy | public | 1 | 1 | write_batch | def write_batch(self,trainer: Trainer,pl_module: LightningModule,prediction: Any,batch_indices: Sequence[int] | None,batch: Any,batch_idx: int,dataloader_idx: int,dirpath: Path,) -> None:"""Write tiles to zarr file.Parameters----------trainer : TrainerPyTorch Lightning Trainer.pl_module : LightningModulePyTorch Lightni... | 1 | 12 | 9 | 48 | 0 | 257 | 294 | 257 | self,trainer,pl_module,prediction,batch_indices,batch,batch_idx,dataloader_idx,dirpath | [] | None | {"Expr": 1} | 0 | 33 | 0 | [] | 0 | [] | The function (write_batch) defined within the public class called WriteStrategy, implement an interface, and it inherit another class.The function start at line 257 and ends at 294. It contains 12 lines of code and it has a cyclomatic complexity of 1. It takes 9 parameters, represented as [257.0] and does not return an... |
CAREamics_careamics | CacheTiles | public | 0 | 1 | __init__ | def __init__(self,write_func: WriteFunc,write_extension: str,write_func_kwargs: dict[str, Any],) -> None:"""A strategy for writing image predictions (i.e. un-tiled predictions).Parameters----------write_func : WriteFuncFunction used to save predictions.write_extension : strExtension added to prediction file paths.write... | 1 | 10 | 4 | 59 | 0 | 320 | 342 | 320 | self,write_func,write_extension,write_func_kwargs | [] | None | {"AnnAssign": 5, "Expr": 2} | 2 | 30 | 2 | ["__init__", "super"] | 8,182 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.15197461_googleapis_python_cloud_core.google.cloud._helpers.__init___py._LocalStack.__init__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16798231_kapji_capital_gains_calculator.cgt_calc.exceptions_py.AmountMissi... | The function (__init__) defined within the public class called CacheTiles, that inherit another class.The function start at line 320 and ends at 342. It contains 10 lines of code and it has a cyclomatic complexity of 1. It takes 4 parameters, represented as [320.0] and does not return any value. It declares 2.0 functio... |
CAREamics_careamics | WriteStrategy | public | 1 | 1 | write_batch | def write_batch(self,trainer: Trainer,pl_module: LightningModule,prediction: NDArray,batch_indices: Sequence[int] | None,batch: NDArray,batch_idx: int,dataloader_idx: int,dirpath: Path,) -> None:"""Save full images.Parameters----------trainer : TrainerPyTorch Lightning Trainer.pl_module : LightningModulePyTorch Lightni... | 4 | 28 | 9 | 175 | 0 | 344 | 399 | 344 | self,trainer,pl_module,prediction,batch_indices,batch,batch_idx,dataloader_idx,dirpath | [] | None | {"Expr": 1} | 0 | 33 | 0 | [] | 0 | [] | The function (write_batch) defined within the public class called WriteStrategy, implement an interface, and it inherit another class.The function start at line 344 and ends at 399. It contains 28 lines of code and it has a cyclomatic complexity of 4. It takes 9 parameters, represented as [344.0] and does not return an... |
CAREamics_careamics | public | public | 0 | 0 | create_write_strategy | def create_write_strategy(write_type: SupportedWriteType,tiled: bool,write_func: WriteFunc | None = None,write_extension: str | None = None,write_func_kwargs: dict[str, Any] | None = None,) -> WriteStrategy:"""Create a write strategy from convenient parameters.Parameters----------write_type : {"tiff", "custom"}The data... | 3 | 28 | 5 | 126 | 4 | 11 | 76 | 11 | write_type,tiled,write_func,write_extension,write_func_kwargs | ['write_func', 'write_extension', 'write_strategy', 'write_func_kwargs'] | WriteStrategy | {"AnnAssign": 1, "Assign": 5, "Expr": 1, "If": 2, "Return": 1} | 4 | 66 | 4 | ["select_write_func", "select_write_extension", "WriteImage", "_create_tiled_write_strategy"] | 7 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lightning.callbacks.prediction_writer_callback.prediction_writer_callback_py.PredictionWriterCallback.from_write_func_params", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3... | The function (create_write_strategy) defined within the public class called public.The function start at line 11 and ends at 76. It contains 28 lines of code and it has a cyclomatic complexity of 3. It takes 5 parameters, represented as [11.0] and does not return any value. It declares 4.0 functions, It has 4.0 functio... |
CAREamics_careamics | public | public | 0 | 0 | _create_tiled_write_strategy | def _create_tiled_write_strategy(write_type: SupportedWriteType,write_func: WriteFunc | None,write_extension: str | None,write_func_kwargs: dict[str, Any],) -> WriteStrategy:"""Create a tiled write strategy.Either `CacheTiles` for caching tiles until a whole image is predicted or`WriteTilesZarr` for writing tiles direc... | 2 | 18 | 4 | 84 | 2 | 79 | 129 | 79 | write_type,write_func,write_extension,write_func_kwargs | ['write_func', 'write_extension'] | WriteStrategy | {"Assign": 2, "Expr": 1, "If": 1, "Return": 1} | 4 | 51 | 4 | ["NotImplementedError", "select_write_func", "select_write_extension", "CacheTiles"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lightning.callbacks.prediction_writer_callback.write_strategy_factory_py.create_write_strategy"] | The function (_create_tiled_write_strategy) defined within the public class called public.The function start at line 79 and ends at 129. It contains 18 lines of code and it has a cyclomatic complexity of 2. It takes 4 parameters, represented as [79.0] and does not return any value. It declares 4.0 functions, It has 4.0... |
CAREamics_careamics | public | public | 0 | 0 | select_write_func | def select_write_func(write_type: SupportedWriteType, write_func: WriteFunc | None = None) -> WriteFunc:"""Return a function to write images.If `write_type` is "custom" then `write_func`, otherwise the known write functionis selected.Parameters----------write_type : {"tiff", "custom"}The data type to save as, includes ... | 3 | 13 | 2 | 50 | 1 | 132 | 176 | 132 | write_type,write_func | ['write_func'] | WriteFunc | {"Assign": 2, "Expr": 1, "If": 2, "Return": 1} | 2 | 45 | 2 | ["ValueError", "get_write_func"] | 4 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lightning.callbacks.prediction_writer_callback.write_strategy_factory_py._create_tiled_write_strategy", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_car... | The function (select_write_func) defined within the public class called public.The function start at line 132 and ends at 176. It contains 13 lines of code and it has a cyclomatic complexity of 3. It takes 2 parameters, represented as [132.0] and does not return any value. It declares 2.0 functions, It has 2.0 function... |
CAREamics_careamics | public | public | 0 | 0 | select_write_extension | def select_write_extension(write_type: SupportedWriteType, write_extension: str | None = None) -> str:"""Return an extension to add to file paths.If `write_type` is "custom" then `write_extension`, otherwise the knownwrite extension is selected.Parameters----------write_type : {"tiff", "custom"}The data type to save as... | 3 | 12 | 2 | 60 | 1 | 179 | 215 | 179 | write_type,write_extension | ['write_extension'] | str | {"AnnAssign": 1, "Assign": 2, "Expr": 1, "If": 2, "Return": 1} | 3 | 37 | 3 | ["SupportedData", "ValueError", "write_type_.get_extension"] | 4 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lightning.callbacks.prediction_writer_callback.write_strategy_factory_py._create_tiled_write_strategy", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_car... | The function (select_write_extension) defined within the public class called public.The function start at line 179 and ends at 215. It contains 12 lines of code and it has a cyclomatic complexity of 3. It takes 2 parameters, represented as [179.0] and does not return any value. It declares 3.0 functions, It has 3.0 fun... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | __init__ | def __init__(self,data_config: NGDataConfig,*,train_data: Any | None = None,train_data_target: Any | None = None,val_data: Any | None = None,val_data_target: Any | None = None,pred_data: Any | None = None,pred_data_target: Any | None = None,read_source_func: Callable | None = None,read_kwargs: dict[str, Any] | None = N... | 5 | 46 | 16 | 286 | 0 | 178 | 278 | 178 | self,data_config,train_data,train_data_target,val_data,val_data_target,pred_data,pred_data_target,extension_filter,val_percentage,val_minimum_split,use_in_memory | [] | None | {"Expr": 1} | 0 | 15 | 0 | [] | 8,182 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.15197461_googleapis_python_cloud_core.google.cloud._helpers.__init___py._LocalStack.__init__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16798231_kapji_capital_gains_calculator.cgt_calc.exceptions_py.AmountMissi... | The function (__init__) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 178 and ends at 278. It contains 46 lines of code and it has a cyclomatic complexity of 5. It takes 16 parameters, represented as [178.0] and does not return any value. It has 8182.0... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | _validate_input_target_type_consistency | def _validate_input_target_type_consistency(self,input_data: InputType,target_data: InputType | None,) -> None:"""Validate if the input and target data types are consistent.Parameters----------input_data : InputTypeInput data, can be a path to a folder, a list of paths, or a numpy array.target_data : Optional[InputType... | 8 | 22 | 3 | 110 | 0 | 280 | 311 | 280 | self,input_data,target_data | [] | None | {"Expr": 1, "If": 5} | 17 | 32 | 17 | ["isinstance", "type", "ValueError", "type", "type", "isinstance", "isinstance", "len", "len", "ValueError", "len", "len", "isinstance", "type", "ValueError", "type", "type"] | 0 | [] | The function (_validate_input_target_type_consistency) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 280 and ends at 311. It contains 22 lines of code and it has a cyclomatic complexity of 8. It takes 3 parameters, represented as [280.0] and does not r... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | _list_files_in_directory | def _list_files_in_directory(self,input_data,target_data=None,) -> tuple[list[Path], list[Path] | None]:"""List files from input and target directories.Parameters----------input_data : InputTypeInput data, can be a path to a folder, a list of paths, or a numpy array.target_data : Optional[InputType]Target data, can be ... | 2 | 16 | 3 | 89 | 0 | 313 | 344 | 313 | self,input_data,target_data | [] | tuple[list[Path], list[Path] | None] | {"Assign": 4, "Expr": 2, "If": 1, "Return": 2} | 5 | 32 | 5 | ["Path", "list_files", "Path", "list_files", "validate_source_target_files"] | 0 | [] | The function (_list_files_in_directory) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 313 and ends at 344. It contains 16 lines of code and it has a cyclomatic complexity of 2. It takes 3 parameters, represented as [313.0] and does not return any value... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | _convert_paths_to_pathlib | def _convert_paths_to_pathlib(self,input_data,target_data=None,) -> tuple[list[Path], list[Path] | None]:"""Create a list of file paths from the input and target data.Parameters----------input_data : InputTypeInput data, can be a path to a folder, a list of paths, or a numpy array.target_data : Optional[InputType]Targe... | 6 | 16 | 3 | 91 | 0 | 346 | 377 | 346 | self,input_data,target_data | [] | tuple[list[Path], list[Path] | None] | {"Assign": 2, "Expr": 2, "If": 1, "Return": 2} | 5 | 32 | 5 | ["isinstance", "Path", "isinstance", "Path", "validate_source_target_files"] | 0 | [] | The function (_convert_paths_to_pathlib) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 346 and ends at 377. It contains 16 lines of code and it has a cyclomatic complexity of 6. It takes 3 parameters, represented as [346.0] and does not return any valu... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | _validate_array_input | def _validate_array_input(self,input_data: InputType,target_data: InputType | None,) -> tuple[Any, Any]:"""Validate if the input data is a numpy array.Parameters----------input_data : InputTypeInput data, can be a path to a folder, a list of paths, or a numpy array.target_data : Optional[InputType]Target data, can be N... | 4 | 15 | 3 | 75 | 0 | 379 | 408 | 379 | self,input_data,target_data | [] | tuple[Any, Any] | {"Assign": 2, "Expr": 1, "If": 2, "Return": 2} | 4 | 30 | 4 | ["isinstance", "isinstance", "ValueError", "type"] | 0 | [] | The function (_validate_array_input) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 379 and ends at 408. It contains 15 lines of code and it has a cyclomatic complexity of 4. It takes 3 parameters, represented as [379.0] and does not return any value. I... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | _validate_path_input | def _validate_path_input(self, input_data: InputType, target_data: InputType | None) -> tuple[list[Path], list[Path] | None]:"""Validate if the input data is a path or a list of paths.Parameters----------input_data : InputTypeInput data, can be a path to a folder, a list of paths, or a numpy array.target_data : Optiona... | 5 | 21 | 3 | 117 | 0 | 410 | 446 | 410 | self,input_data,target_data | [] | tuple[list[Path], list[Path] | None] | {"Assign": 2, "Expr": 1, "If": 4, "Return": 2} | 8 | 37 | 8 | ["isinstance", "isinstance", "self._list_files_in_directory", "isinstance", "isinstance", "self._convert_paths_to_pathlib", "ValueError", "type"] | 0 | [] | The function (_validate_path_input) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 410 and ends at 446. It contains 21 lines of code and it has a cyclomatic complexity of 5. It takes 3 parameters, represented as [410.0] and does not return any value. It... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | _validate_custom_input | def _validate_custom_input(self, input_data, target_data) -> tuple[Any, Any]:"""Convert custom input data to a list of file paths.Parameters----------input_data : InputTypeInput data, can be a path to a folder, a list of paths, or a numpy array.target_data : Optional[InputType]Target data, can be None, a path to a fold... | 7 | 24 | 3 | 134 | 0 | 448 | 487 | 448 | self,input_data,target_data | [] | tuple[Any, Any] | {"Assign": 2, "Expr": 1, "If": 6, "Return": 4} | 8 | 40 | 8 | ["isinstance", "isinstance", "self._list_files_in_directory", "isinstance", "isinstance", "isinstance", "self._convert_paths_to_pathlib", "ValueError"] | 0 | [] | The function (_validate_custom_input) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 448 and ends at 487. It contains 24 lines of code and it has a cyclomatic complexity of 7. It takes 3 parameters, represented as [448.0] and does not return any value. ... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | _initialize_data_pair | def _initialize_data_pair(self,input_data: InputType | None,target_data: InputType | None,) -> tuple[Any, Any]:"""Initialize a pair of input and target data.Parameters----------input_data : InputTypeInput data, can be None, a path to a folder, a list of paths, or a numpyarray.target_data : Optional[InputType]Target dat... | 11 | 42 | 3 | 227 | 0 | 489 | 552 | 489 | self,input_data,target_data | [] | tuple[Any, Any] | {"Expr": 2, "If": 10, "Return": 6} | 21 | 64 | 21 | ["self._validate_input_target_type_consistency", "isinstance", "self._validate_array_input", "isinstance", "isinstance", "self._validate_array_input", "ValueError", "type", "ValueError", "type", "isinstance", "self._validate_path_input", "isinstance", "isinstance", "self._validate_path_input", "ValueError", "type", "Va... | 0 | [] | The function (_initialize_data_pair) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 489 and ends at 552. It contains 42 lines of code and it has a cyclomatic complexity of 11. It takes 3 parameters, represented as [489.0] and does not return any value. ... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | setup | def setup(self, stage: str) -> None:"""Setup datasets.Lightning hook that is called at the beginning of fit (train + validate),validate, test, or predict. Creates the datasets for a given stage.Parameters----------stage : strThe stage to set up datasets for.Is either 'fit', 'validate', 'test', or 'predict'.Raises------... | 4 | 59 | 2 | 345 | 0 | 554 | 630 | 554 | self,stage | [] | None | {"Assign": 7, "Expr": 2, "If": 3} | 6 | 77 | 6 | ["create_dataset", "self.config.set_means_and_stds", "create_dataset", "create_dataset", "create_dataset", "NotImplementedError"] | 23 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16418165_szabgab_pydigger_com.PyDigger.fetch_py.main", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.3584344_influxgraph_influxgraph.setup_py.run_setup", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.... | The function (setup) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 554 and ends at 630. It contains 59 lines of code and it has a cyclomatic complexity of 4. It takes 2 parameters, represented as [554.0] and does not return any value. It declares 6.0 f... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | train_dataloader | def train_dataloader(self) -> DataLoader:"""Create a dataloader for training.Returns-------DataLoaderTraining dataloader."""return DataLoader(self.train_dataset,batch_size=self.batch_size,collate_fn=default_collate,**self.config.train_dataloader_params,) | 1 | 7 | 1 | 33 | 0 | 632 | 646 | 632 | self | [] | DataLoader | {"Expr": 1, "Return": 1} | 1 | 15 | 1 | ["DataLoader"] | 0 | [] | The function (train_dataloader) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 632 and ends at 646. It contains 7 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters and does not return any value. It declare ... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | val_dataloader | def val_dataloader(self) -> DataLoader:"""Create a dataloader for validation.Returns-------DataLoaderValidation dataloader."""return DataLoader(self.val_dataset,batch_size=self.batch_size,collate_fn=default_collate,**self.config.val_dataloader_params,) | 1 | 7 | 1 | 33 | 0 | 648 | 662 | 648 | self | [] | DataLoader | {"Expr": 1, "Return": 1} | 1 | 15 | 1 | ["DataLoader"] | 0 | [] | The function (val_dataloader) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 648 and ends at 662. It contains 7 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters and does not return any value. It declare 1.... |
CAREamics_careamics | CareamicsDataModule | public | 0 | 1 | predict_dataloader | def predict_dataloader(self) -> DataLoader:"""Create a dataloader for prediction.Returns-------DataLoaderPrediction dataloader."""return DataLoader(self.predict_dataset,batch_size=self.batch_size,collate_fn=default_collate,**self.config.test_dataloader_params,) | 1 | 7 | 1 | 33 | 0 | 664 | 678 | 664 | self | [] | DataLoader | {"Expr": 1, "Return": 1} | 1 | 15 | 1 | ["DataLoader"] | 0 | [] | The function (predict_dataloader) defined within the public class called CareamicsDataModule, that inherit another class.The function start at line 664 and ends at 678. It contains 7 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters and does not return any value. It declar... |
CAREamics_careamics | CAREModule | public | 0 | 1 | __init__ | def __init__(self, algorithm_config: Union[CAREAlgorithm, dict]) -> None:"""Instantiate CARE DataModule.Parameters----------algorithm_config : CAREAlgorithm or dictConfiguration for the CARE algorithm, either as a CAREAlgorithm instance ora dictionary."""super().__init__(algorithm_config)assert isinstance(algorithm_con... | 3 | 12 | 2 | 75 | 0 | 28 | 47 | 28 | self,algorithm_config | [] | None | {"AnnAssign": 1, "Assign": 2, "Expr": 2, "If": 2} | 4 | 20 | 4 | ["__init__", "super", "isinstance", "ValueError"] | 8,182 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.15197461_googleapis_python_cloud_core.google.cloud._helpers.__init___py._LocalStack.__init__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16798231_kapji_capital_gains_calculator.cgt_calc.exceptions_py.AmountMissi... | The function (__init__) defined within the public class called CAREModule, that inherit another class.The function start at line 28 and ends at 47. It contains 12 lines of code and it has a cyclomatic complexity of 3. It takes 2 parameters, represented as [28.0] and does not return any value. It declares 4.0 functions,... |
CAREamics_careamics | CAREModule | public | 0 | 1 | training_step | def training_step(self,batch: tuple[ImageRegionData, ImageRegionData],batch_idx: Any,) -> Any:"""Training step for CARE module.Parameters----------batch : (ImageRegionData, ImageRegionData)A tuple containing the input data and the target data.batch_idx : AnyThe index of the current batch in the training loop.Returns---... | 1 | 10 | 3 | 76 | 0 | 49 | 76 | 49 | self,batch,batch_idx | [] | Any | {"Assign": 3, "Expr": 2, "Return": 1} | 3 | 28 | 3 | ["self.model", "self.loss_func", "self._log_training_stats"] | 0 | [] | The function (training_step) defined within the public class called CAREModule, that inherit another class.The function start at line 49 and ends at 76. It contains 10 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [49.0] and does not return any value. It declares 3.0 funct... |
CAREamics_careamics | CAREModule | public | 0 | 1 | validation_step | def validation_step(self,batch: tuple[ImageRegionData, ImageRegionData],batch_idx: Any,) -> None:"""Validation step for CARE module.Parameters----------batch : (ImageRegionData, ImageRegionData)A tuple containing the input data and the target data.batch_idx : AnyThe index of the current batch in the training loop."""x,... | 1 | 10 | 3 | 84 | 0 | 78 | 97 | 78 | self,batch,batch_idx | [] | None | {"Assign": 3, "Expr": 3} | 4 | 20 | 4 | ["self.model", "self.loss_func", "self.metrics", "self._log_validation_stats"] | 0 | [] | The function (validation_step) defined within the public class called CAREModule, that inherit another class.The function start at line 78 and ends at 97. It contains 10 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [78.0] and does not return any value. It declares 4.0 fun... |
CAREamics_careamics | N2VModule | public | 0 | 1 | __init__ | def __init__(self, algorithm_config: Union[N2VAlgorithm, dict]) -> None:"""Instantiate N2V DataModule.Parameters----------algorithm_config : N2VAlgorithm or dictConfiguration for the N2V algorithm, either as an N2VAlgorithm instance or adictionary."""super().__init__(algorithm_config)assert isinstance(algorithm_config,... | 1 | 9 | 2 | 51 | 0 | 28 | 46 | 28 | self,algorithm_config | [] | None | {"Assign": 2, "Expr": 2} | 4 | 19 | 4 | ["__init__", "super", "isinstance", "N2VManipulateTorch"] | 8,182 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.15197461_googleapis_python_cloud_core.google.cloud._helpers.__init___py._LocalStack.__init__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16798231_kapji_capital_gains_calculator.cgt_calc.exceptions_py.AmountMissi... | The function (__init__) defined within the public class called N2VModule, that inherit another class.The function start at line 28 and ends at 46. It contains 9 lines of code and it has a cyclomatic complexity of 1. It takes 2 parameters, represented as [28.0] and does not return any value. It declares 4.0 functions, I... |
CAREamics_careamics | N2VModule | public | 0 | 1 | _load_best_checkpoint | def _load_best_checkpoint(self) -> None:"""Load the best checkpoint for N2V model."""logger.warning("Loading best checkpoint for N2V model. Note that for N2V, ""the checkpoint with the best validation metrics may not necessarily ""have the best denoising performance.")super()._load_best_checkpoint() | 1 | 7 | 1 | 23 | 0 | 48 | 55 | 48 | self | [] | None | {"Expr": 3} | 3 | 8 | 3 | ["logger.warning", "_load_best_checkpoint", "super"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lightning.dataset_ng.lightning_modules.n2v_module_py.N2VModule._load_best_checkpoint"] | The function (_load_best_checkpoint) defined within the public class called N2VModule, that inherit another class.The function start at line 48 and ends at 55. It contains 7 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters and does not return any value. It declares 3.0 fu... |
CAREamics_careamics | N2VModule | public | 0 | 1 | training_step | def training_step(self,batch: Union[tuple[ImageRegionData], tuple[ImageRegionData, ImageRegionData]],batch_idx: Any,) -> Any:"""Training step for N2V model.Parameters----------batch : ImageRegionData or (ImageRegionData, ImageRegionData)A tuple containing the input data and the target data.batch_idx : AnyThe index of t... | 1 | 11 | 3 | 89 | 0 | 57 | 83 | 57 | self,batch,batch_idx | [] | Any | {"Assign": 4, "Expr": 2, "Return": 1} | 4 | 27 | 4 | ["self.n2v_manipulate", "self.model", "self.loss_func", "self._log_training_stats"] | 0 | [] | The function (training_step) defined within the public class called N2VModule, that inherit another class.The function start at line 57 and ends at 83. It contains 11 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [57.0] and does not return any value. It declares 4.0 functi... |
CAREamics_careamics | N2VModule | public | 0 | 1 | validation_step | def validation_step(self,batch: Union[tuple[ImageRegionData], tuple[ImageRegionData, ImageRegionData]],batch_idx: Any,) -> None:"""Validation step for N2V model.Parameters----------batch : ImageRegionData or (ImageRegionData, ImageRegionData)A tuple containing the input data and the target data.batch_idx : AnyThe index... | 1 | 11 | 3 | 95 | 0 | 85 | 106 | 85 | self,batch,batch_idx | [] | None | {"Assign": 4, "Expr": 3} | 5 | 22 | 5 | ["self.n2v_manipulate", "self.model", "self.loss_func", "self.metrics", "self._log_validation_stats"] | 0 | [] | The function (validation_step) defined within the public class called N2VModule, that inherit another class.The function start at line 85 and ends at 106. It contains 11 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [85.0] and does not return any value. It declares 5.0 fun... |
CAREamics_careamics | UnetModule | public | 0 | 1 | __init__ | def __init__(self, algorithm_config: Union[CAREAlgorithm, N2VAlgorithm, N2NAlgorithm, dict]) -> None:"""Instantiate UNet DataModule.Parameters----------algorithm_config : CAREAlgorithm, N2VAlgorithm, N2NAlgorithm, or dictConfiguration for the algorithm, either as an instance of a specificalgorithm class or a dictionary... | 2 | 10 | 2 | 81 | 0 | 32 | 55 | 32 | self,algorithm_config | [] | None | {"AnnAssign": 1, "Assign": 4, "Expr": 2, "If": 1} | 8 | 24 | 8 | ["__init__", "super", "isinstance", "algorithm_factory", "UNet", "algorithm_config.model.model_dump", "MetricCollection", "PeakSignalNoiseRatio"] | 8,182 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.15197461_googleapis_python_cloud_core.google.cloud._helpers.__init___py._LocalStack.__init__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16798231_kapji_capital_gains_calculator.cgt_calc.exceptions_py.AmountMissi... | The function (__init__) defined within the public class called UnetModule, that inherit another class.The function start at line 32 and ends at 55. It contains 10 lines of code and it has a cyclomatic complexity of 2. It takes 2 parameters, represented as [32.0] and does not return any value. It declares 8.0 functions,... |
CAREamics_careamics | UnetModule | public | 0 | 1 | forward | def forward(self, x: Any) -> Any:"""Default forward method.Parameters----------x : AnyInput data.Returns-------AnyOutput from the model."""return self.model(x) | 1 | 2 | 2 | 19 | 0 | 57 | 70 | 57 | self,x | [] | Any | {"Expr": 1, "Return": 1} | 1 | 14 | 1 | ["self.model"] | 54 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.3646986_mapbox_mapbox_sdk_py.tests.test_geocoder_py.test_geocoder_forward", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.3646986_mapbox_mapbox_sdk_py.tests.test_geocoder_py.test_geocoder_forward_bbox", "_.content.g... | The function (forward) defined within the public class called UnetModule, that inherit another class.The function start at line 57 and ends at 70. It contains 2 lines of code and it has a cyclomatic complexity of 1. It takes 2 parameters, represented as [57.0] and does not return any value. It declare 1.0 function, It ... |
CAREamics_careamics | UnetModule | public | 0 | 1 | _log_training_stats | def _log_training_stats(self, loss: Any, batch_size: Any) -> None:"""Log training statistics.Parameters----------loss : AnyThe loss value for the current training step.batch_size : AnyThe size of the batch used in the current training step."""self.log("train_loss",loss,on_step=True,on_epoch=True,prog_bar=True,logger=Tr... | 2 | 23 | 3 | 112 | 0 | 72 | 104 | 72 | self,loss,batch_size | [] | None | {"Assign": 3, "Expr": 3, "If": 1} | 4 | 33 | 4 | ["self.log", "self.optimizers", "isinstance", "self.log"] | 0 | [] | The function (_log_training_stats) defined within the public class called UnetModule, that inherit another class.The function start at line 72 and ends at 104. It contains 23 lines of code and it has a cyclomatic complexity of 2. It takes 3 parameters, represented as [72.0] and does not return any value. It declares 4.... |
CAREamics_careamics | UnetModule | public | 0 | 1 | _log_validation_stats | def _log_validation_stats(self, loss: Any, batch_size: Any) -> None:"""Log validation statistics.Parameters----------loss : AnyThe loss value for the current validation step.batch_size : AnyThe size of the batch used in the current validation step."""self.log("val_loss",loss,on_step=False,on_epoch=True,prog_bar=True,lo... | 1 | 11 | 3 | 65 | 0 | 106 | 125 | 106 | self,loss,batch_size | [] | None | {"Expr": 3} | 2 | 20 | 2 | ["self.log", "self.log_dict"] | 0 | [] | The function (_log_validation_stats) defined within the public class called UnetModule, that inherit another class.The function start at line 106 and ends at 125. It contains 11 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [106.0] and does not return any value. It declare... |
CAREamics_careamics | UnetModule | public | 0 | 1 | _load_best_checkpoint | def _load_best_checkpoint(self) -> None:"""Load the best checkpoint from the trainer's checkpoint callback."""if (not hasattr(self.trainer, "checkpoint_callback")or self.trainer.checkpoint_callback is None):logger.warning("No checkpoint callback found, cannot load best checkpoint.")returnbest_model_path = self.trainer.... | 5 | 14 | 1 | 88 | 0 | 127 | 142 | 127 | self | [] | None | {"Assign": 2, "Expr": 5, "If": 2, "Return": 1} | 6 | 16 | 6 | ["hasattr", "logger.warning", "logger.info", "torch.load", "self.load_state_dict", "logger.warning"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lightning.dataset_ng.lightning_modules.n2v_module_py.N2VModule._load_best_checkpoint"] | The function (_load_best_checkpoint) defined within the public class called UnetModule, that inherit another class.The function start at line 127 and ends at 142. It contains 14 lines of code and it has a cyclomatic complexity of 5. The function does not take any parameters and does not return any value. It declares 6.... |
CAREamics_careamics | UnetModule | public | 0 | 1 | predict_step | def predict_step(self,batch: Union[tuple[ImageRegionData], tuple[ImageRegionData, ImageRegionData]],batch_idx: Any,load_best_checkpoint=False,) -> Any:"""Default predict step.Parameters----------batch : ImageRegionData or (ImageRegionData, ImageRegionData)A tuple containing the input data and optionally the target data... | 3 | 27 | 4 | 159 | 0 | 144 | 190 | 144 | self,batch,batch_idx,load_best_checkpoint | [] | Any | {"Assign": 8, "Expr": 2, "If": 1, "Return": 1} | 7 | 47 | 7 | ["self._load_best_checkpoint", "numpy", "cpu", "self.model", "Denormalize", "denormalize", "ImageRegionData"] | 0 | [] | The function (predict_step) defined within the public class called UnetModule, that inherit another class.The function start at line 144 and ends at 190. It contains 27 lines of code and it has a cyclomatic complexity of 3. It takes 4 parameters, represented as [144.0] and does not return any value. It declares 7.0 fun... |
CAREamics_careamics | UnetModule | public | 0 | 1 | configure_optimizers | def configure_optimizers(self) -> Any:"""Configure optimizers.Returns-------AnyA dictionary containing the optimizer and learning rate scheduler."""optimizer_func = get_optimizer(self.config.optimizer.name)optimizer = optimizer_func(self.model.parameters(), **self.config.optimizer.parameters)scheduler_func = get_schedu... | 1 | 12 | 1 | 83 | 0 | 192 | 212 | 192 | self | [] | Any | {"Assign": 4, "Expr": 1, "Return": 1} | 5 | 21 | 5 | ["get_optimizer", "optimizer_func", "self.model.parameters", "get_scheduler", "scheduler_func"] | 0 | [] | The function (configure_optimizers) defined within the public class called UnetModule, that inherit another class.The function start at line 192 and ends at 212. It contains 12 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters and does not return any value. It declares 5.0... |
CAREamics_careamics | public | public | 0 | 0 | loss_factory | def loss_factory(loss: Union[SupportedLoss, str]) -> Callable:"""Return loss function.Parameters----------loss : Union[SupportedLoss, str]Requested loss.Returns-------CallableLoss function.Raises------NotImplementedErrorIf the loss is unknown."""if loss == SupportedLoss.N2V:return n2v_loss# elif loss_type == SupportedL... | 8 | 17 | 1 | 86 | 0 | 37 | 80 | 37 | loss | [] | Callable | {"Expr": 1, "If": 7, "Return": 7} | 1 | 44 | 1 | ["NotImplementedError"] | 3 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lightning.lightning_module_py.FCNModule.__init__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lightning.lightning_module_py.VA... | The function (loss_factory) defined within the public class called public.The function start at line 37 and ends at 80. It contains 17 lines of code and it has a cyclomatic complexity of 8. The function does not take any parameters and does not return any value. It declare 1.0 function, It has 1.0 function called insid... |
CAREamics_careamics | public | public | 0 | 0 | mse_loss | def mse_loss(source: torch.Tensor, target: torch.Tensor, *args) -> torch.Tensor:"""Mean squared error loss.Parameters----------source : torch.TensorSource patches.target : torch.TensorTarget patches.*args : AnyAdditional arguments.Returns-------torch.TensorLoss value."""loss = MSELoss()return loss(source, target) | 1 | 3 | 3 | 35 | 1 | 11 | 30 | 11 | source,target,*args | ['loss'] | torch.Tensor | {"Assign": 1, "Expr": 1, "Return": 1} | 2 | 20 | 2 | ["MSELoss", "loss"] | 0 | [] | The function (mse_loss) defined within the public class called public.The function start at line 11 and ends at 30. It contains 3 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [11.0] and does not return any value. It declares 2.0 functions, and It has 2.0 functions called... |
CAREamics_careamics | public | public | 0 | 0 | n2v_loss | def n2v_loss(manipulated_batch: torch.Tensor,original_batch: torch.Tensor,masks: torch.Tensor,*args,) -> torch.Tensor:"""N2V Loss function described in A Krull et al 2018.Parameters----------manipulated_batch : torch.TensorBatch after manipulation function applied.original_batch : torch.TensorOriginal images.masks : to... | 1 | 9 | 4 | 58 | 2 | 33 | 61 | 33 | manipulated_batch,original_batch,masks,*args | ['errors', 'loss'] | torch.Tensor | {"Assign": 2, "Expr": 1, "Return": 1} | 2 | 29 | 2 | ["torch.sum", "torch.sum"] | 0 | [] | The function (n2v_loss) defined within the public class called public.The function start at line 33 and ends at 61. It contains 9 lines of code and it has a cyclomatic complexity of 1. It takes 4 parameters, represented as [33.0] and does not return any value. It declares 2.0 functions, and It has 2.0 functions called... |
CAREamics_careamics | public | public | 0 | 0 | mae_loss | def mae_loss(samples: torch.Tensor, labels: torch.Tensor, *args) -> torch.Tensor:"""N2N Loss function described in to J Lehtinen et al 2018.Parameters----------samples : torch.TensorRaw patches.labels : torch.TensorDifferent subset of noisy patches.*args : AnyAdditional arguments.Returns-------torch.TensorLoss value.""... | 1 | 3 | 3 | 35 | 1 | 64 | 83 | 64 | samples,labels,*args | ['loss'] | torch.Tensor | {"Assign": 1, "Expr": 1, "Return": 1} | 2 | 20 | 2 | ["L1Loss", "loss"] | 0 | [] | The function (mae_loss) defined within the public class called public.The function start at line 64 and ends at 83. It contains 3 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [64.0] and does not return any value. It declares 2.0 functions, and It has 2.0 functions called... |
CAREamics_careamics | public | public | 0 | 0 | free_bits_kl | def free_bits_kl(kl: torch.Tensor, free_bits: float, batch_average: bool = False, eps: float = 1e-6) -> torch.Tensor:"""Compute free-bits version of KL divergence.This function ensures that the KL doesn't go to zero for any latent dimension.Hence, it contributes to use latent variables more efficiently, leading tobette... | 3 | 9 | 4 | 83 | 0 | 4 | 44 | 4 | kl,free_bits,batch_average,eps | [] | torch.Tensor | {"Expr": 1, "If": 2, "Return": 3} | 6 | 41 | 6 | ["kl.dim", "kl.mean", "clamp", "kl.mean", "mean", "kl.clamp"] | 3 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_py.get_kl_divergence_loss", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.lightning_module_py.La... | The function (free_bits_kl) defined within the public class called public.The function start at line 4 and ends at 44. It contains 9 lines of code and it has a cyclomatic complexity of 3. It takes 4 parameters, represented as [4.0] and does not return any value. It declares 6.0 functions, It has 6.0 functions called in... |
CAREamics_careamics | public | public | 0 | 0 | get_kl_weight | def get_kl_weight(kl_annealing: bool,kl_start: int,kl_annealtime: int,kl_weight: float,current_epoch: int,) -> float:"""Compute the weight of the KL loss in case of annealing.Parameters----------kl_annealing : boolWhether to use KL annealing.kl_start : intThe epoch at which to startkl_annealtime : intThe number of epoc... | 4 | 17 | 5 | 90 | 1 | 47 | 83 | 47 | kl_annealing,kl_start,kl_annealtime,kl_weight,current_epoch | ['kl_weight'] | float | {"Assign": 4, "Expr": 1, "If": 3, "Return": 2} | 2 | 37 | 2 | ["min", "max"] | 3 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_py.denoisplit_loss", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_py.hdn_loss", "_.content... | The function (get_kl_weight) defined within the public class called public.The function start at line 47 and ends at 83. It contains 17 lines of code and it has a cyclomatic complexity of 4. It takes 5 parameters, represented as [47.0] and does not return any value. It declares 2.0 functions, It has 2.0 functions calle... |
CAREamics_careamics | public | public | 0 | 0 | get_reconstruction_loss | def get_reconstruction_loss(reconstruction: torch.Tensor,target: torch.Tensor,likelihood_obj: Likelihood,) -> dict[str, torch.Tensor]:"""Compute the reconstruction loss (negative log-likelihood).Parameters----------reconstruction: torch.TensorThe output of the LVAE decoder. Shape is (B, C, [Z], Y, X), where C is thenum... | 1 | 7 | 3 | 49 | 0 | 23 | 49 | 23 | reconstruction,target,likelihood_obj | [] | dict[str, torch.Tensor] | {"Assign": 1, "Expr": 1, "Return": 1} | 2 | 27 | 2 | ["likelihood_obj", "ll.mean"] | 5 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_py._reconstruction_loss_musplit_denoisplit", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_... | The function (get_reconstruction_loss) defined within the public class called public.The function start at line 23 and ends at 49. It contains 7 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [23.0] and does not return any value. It declares 2.0 functions, It has 2.0 functi... |
CAREamics_careamics | public | public | 0 | 0 | _reconstruction_loss_musplit_denoisplit | def _reconstruction_loss_musplit_denoisplit(predictions: Union[torch.Tensor, tuple[torch.Tensor, torch.Tensor]],targets: torch.Tensor,nm_likelihood: NoiseModelLikelihood,gaussian_likelihood: GaussianLikelihood,nm_weight: float,gaussian_weight: float,) -> torch.Tensor:"""Compute the reconstruction loss for muSplit-denoi... | 2 | 22 | 6 | 131 | 4 | 52 | 107 | 52 | predictions,targets,nm_likelihood,gaussian_likelihood,nm_weight,gaussian_weight | ['recons_loss_gm', 'recons_loss_nm', 'recons_loss', 'pred_mean'] | torch.Tensor | {"Assign": 5, "Expr": 1, "If": 1, "Return": 1} | 3 | 56 | 3 | ["predictions.chunk", "get_reconstruction_loss", "get_reconstruction_loss"] | 2 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_py.denoisplit_musplit_loss", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.tests.losses.test_lvae_losses_py.test_reconstruct... | The function (_reconstruction_loss_musplit_denoisplit) defined within the public class called public.The function start at line 52 and ends at 107. It contains 22 lines of code and it has a cyclomatic complexity of 2. It takes 6 parameters, represented as [52.0] and does not return any value. It declares 3.0 functions,... |
CAREamics_careamics | public | public | 0 | 0 | get_kl_divergence_loss | def get_kl_divergence_loss(kl_type: Literal["kl", "kl_restricted"],topdown_data: dict[str, torch.Tensor],rescaling: Literal["latent_dim", "image_dim"],aggregation: Literal["mean", "sum"],free_bits_coeff: float,img_shape: tuple[int] | None = None,) -> torch.Tensor:"""Compute the KL divergence loss.NOTE: Description of `... | 8 | 27 | 6 | 209 | 3 | 110 | 195 | 110 | kl_type,topdown_data,rescaling,aggregation,free_bits_coeff,img_shape | ['latent_dim', 'kl', 'norm_factor'] | torch.Tensor | {"Assign": 9, "Expr": 1, "For": 1, "If": 5, "Return": 1} | 10 | 86 | 10 | ["torch.cat", "kl_layer.unsqueeze", "free_bits_kl", "len", "range", "len", "np.prod", "np.prod", "kl.mean", "kl.sum"] | 3 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_py._get_kl_divergence_loss_denoisplit", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_py._g... | The function (get_kl_divergence_loss) defined within the public class called public.The function start at line 110 and ends at 195. It contains 27 lines of code and it has a cyclomatic complexity of 8. It takes 6 parameters, represented as [110.0] and does not return any value. It declares 10.0 functions, It has 10.0 f... |
CAREamics_careamics | public | public | 0 | 0 | _get_kl_divergence_loss_musplit | def _get_kl_divergence_loss_musplit(topdown_data: dict[str, torch.Tensor],img_shape: tuple[int],kl_type: Literal["kl", "kl_restricted"],) -> torch.Tensor:"""Compute the KL divergence loss for muSplit.Parameters----------topdown_data : dict[str, torch.Tensor]A dictionary containing information computed for each layer du... | 1 | 13 | 3 | 66 | 0 | 198 | 230 | 198 | topdown_data,img_shape,kl_type | [] | torch.Tensor | {"Expr": 1, "Return": 1} | 1 | 33 | 1 | ["get_kl_divergence_loss"] | 2 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_py.denoisplit_musplit_loss", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_py.musplit_loss"... | The function (_get_kl_divergence_loss_musplit) defined within the public class called public.The function start at line 198 and ends at 230. It contains 13 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [198.0] and does not return any value. It declare 1.0 function, It has ... |
CAREamics_careamics | public | public | 0 | 0 | _get_kl_divergence_loss_denoisplit | def _get_kl_divergence_loss_denoisplit(topdown_data: dict[str, torch.Tensor],img_shape: tuple[int],kl_type: Literal["kl", "kl_restricted"],) -> torch.Tensor:"""Compute the KL divergence loss for denoiSplit.Parameters----------topdown_data : dict[str, torch.Tensor]A dictionary containing information computed for each la... | 1 | 13 | 3 | 66 | 0 | 233 | 265 | 233 | topdown_data,img_shape,kl_type | [] | torch.Tensor | {"Expr": 1, "Return": 1} | 1 | 33 | 1 | ["get_kl_divergence_loss"] | 3 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_py.denoisplit_loss", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.losses.lvae.losses_py.denoisplit_musplit_lo... | The function (_get_kl_divergence_loss_denoisplit) defined within the public class called public.The function start at line 233 and ends at 265. It contains 13 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [233.0] and does not return any value. It declare 1.0 function, It h... |
CAREamics_careamics | public | public | 0 | 0 | hdn_loss | def hdn_loss(model_outputs: tuple[torch.Tensor, dict[str, Any]],targets: torch.Tensor,config: LVAELossConfig,gaussian_likelihood: GaussianLikelihood | None,noise_model_likelihood: NoiseModelLikelihood | None,) -> dict[str, torch.Tensor] | None:"""Loss function for HDN.Parameters----------model_outputs : tuple[torch.Ten... | 6 | 49 | 5 | 244 | 6 | 275 | 354 | 275 | model_outputs,targets,config,gaussian_likelihood,noise_model_likelihood | ['likelihood', 'output', 'net_loss', 'kl_loss', 'recons_loss', 'kl_weight'] | dict[str, torch.Tensor] | None | {"Assign": 9, "Expr": 1, "If": 4, "Return": 2} | 11 | 80 | 11 | ["ValueError", "get_reconstruction_loss", "any", "torch.isnan", "get_kl_weight", "_get_kl_divergence_loss_denoisplit", "isinstance", "recons_loss.detach", "kl_loss.detach", "any", "torch.isnan"] | 0 | [] | The function (hdn_loss) defined within the public class called public.The function start at line 275 and ends at 354. It contains 49 lines of code and it has a cyclomatic complexity of 6. It takes 5 parameters, represented as [275.0] and does not return any value. It declares 11.0 functions, and It has 11.0 functions ... |
CAREamics_careamics | public | public | 0 | 0 | musplit_loss | def musplit_loss(model_outputs: tuple[torch.Tensor, dict[str, Any]],targets: torch.Tensor,config: LVAELossConfig,gaussian_likelihood: GaussianLikelihood | None,noise_model_likelihood: NoiseModelLikelihood | None = None,# TODO: ugly) -> dict[str, torch.Tensor] | None:"""Loss function for muSplit.Parameters----------mode... | 4 | 44 | 5 | 226 | 5 | 357 | 432 | 357 | model_outputs,targets,config,gaussian_likelihood,noise_model_likelihood | ['output', 'net_loss', 'kl_loss', 'recons_loss', 'kl_weight'] | dict[str, torch.Tensor] | None | {"Assign": 7, "Expr": 1, "If": 2, "Return": 2} | 10 | 76 | 10 | ["get_reconstruction_loss", "any", "torch.isnan", "get_kl_weight", "_get_kl_divergence_loss_musplit", "isinstance", "recons_loss.detach", "kl_loss.detach", "any", "torch.isnan"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.tests.losses.test_lvae_losses_py.test_musplit_loss"] | The function (musplit_loss) defined within the public class called public.The function start at line 357 and ends at 432. It contains 44 lines of code and it has a cyclomatic complexity of 4. It takes 5 parameters, represented as [357.0] and does not return any value. It declares 10.0 functions, It has 10.0 functions c... |
CAREamics_careamics | public | public | 0 | 0 | denoisplit_loss | def denoisplit_loss(model_outputs: tuple[torch.Tensor, dict[str, Any]],targets: torch.Tensor,config: LVAELossConfig,gaussian_likelihood: GaussianLikelihood | None = None,noise_model_likelihood: NoiseModelLikelihood | None = None,) -> dict[str, torch.Tensor] | None:"""Loss function for DenoiSplit.Parameters----------mod... | 4 | 44 | 5 | 228 | 5 | 435 | 509 | 435 | model_outputs,targets,config,gaussian_likelihood,noise_model_likelihood | ['output', 'net_loss', 'kl_loss', 'recons_loss', 'kl_weight'] | dict[str, torch.Tensor] | None | {"Assign": 7, "Expr": 1, "If": 2, "Return": 2} | 10 | 75 | 10 | ["get_reconstruction_loss", "any", "torch.isnan", "get_kl_weight", "_get_kl_divergence_loss_denoisplit", "isinstance", "recons_loss.detach", "kl_loss.detach", "any", "torch.isnan"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.tests.losses.test_lvae_losses_py.test_denoisplit_loss"] | The function (denoisplit_loss) defined within the public class called public.The function start at line 435 and ends at 509. It contains 44 lines of code and it has a cyclomatic complexity of 4. It takes 5 parameters, represented as [435.0] and does not return any value. It declares 10.0 functions, It has 10.0 function... |
CAREamics_careamics | public | public | 0 | 0 | denoisplit_musplit_loss | def denoisplit_musplit_loss(model_outputs: tuple[torch.Tensor, dict[str, Any]],targets: torch.Tensor,config: LVAELossConfig,gaussian_likelihood: GaussianLikelihood,noise_model_likelihood: NoiseModelLikelihood,) -> dict[str, torch.Tensor] | None:"""Loss function for DenoiSplit.Parameters----------model_outputs : tuple[t... | 4 | 45 | 5 | 239 | 6 | 512 | 589 | 512 | model_outputs,targets,config,gaussian_likelihood,noise_model_likelihood | ['output', 'net_loss', 'kl_loss', 'recons_loss', 'denoisplit_kl', 'musplit_kl'] | dict[str, torch.Tensor] | None | {"Assign": 9, "Expr": 1, "If": 2, "Return": 2} | 10 | 78 | 10 | ["_reconstruction_loss_musplit_denoisplit", "any", "torch.isnan", "_get_kl_divergence_loss_denoisplit", "_get_kl_divergence_loss_musplit", "isinstance", "recons_loss.detach", "kl_loss.detach", "any", "torch.isnan"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.tests.losses.test_lvae_losses_py.test_denoisplit_musplit_loss"] | The function (denoisplit_musplit_loss) defined within the public class called public.The function start at line 512 and ends at 589. It contains 45 lines of code and it has a cyclomatic complexity of 4. It takes 5 parameters, represented as [512.0] and does not return any value. It declares 10.0 functions, It has 10.0 ... |
CAREamics_careamics | public | public | 0 | 0 | get_last_index | def get_last_index(bin_count, quantile):cumsum = np.cumsum(bin_count)normalized_cumsum = cumsum / cumsum[-1]for i in range(1, len(normalized_cumsum)):if normalized_cumsum[-i] < quantile:return i - 1return None | 3 | 7 | 2 | 52 | 2 | 8 | 14 | 8 | bin_count,quantile | ['normalized_cumsum', 'cumsum'] | Returns | {"Assign": 2, "For": 1, "If": 1, "Return": 2} | 3 | 7 | 3 | ["np.cumsum", "range", "len"] | 3 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.calibration_py.Calibration.get_calibrated_factor_for_stdev", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_tra... | The function (get_last_index) defined within the public class called public.The function start at line 8 and ends at 14. It contains 7 lines of code and it has a cyclomatic complexity of 3. It takes 2 parameters, represented as [8.0], and this function return a value. It declares 3.0 functions, It has 3.0 functions cal... |
CAREamics_careamics | public | public | 0 | 0 | get_first_index | def get_first_index(bin_count, quantile):cumsum = np.cumsum(bin_count)normalized_cumsum = cumsum / cumsum[-1]for i in range(len(normalized_cumsum)):if normalized_cumsum[i] > quantile:return ireturn None | 3 | 7 | 2 | 47 | 2 | 17 | 23 | 17 | bin_count,quantile | ['normalized_cumsum', 'cumsum'] | Returns | {"Assign": 2, "For": 1, "If": 1, "Return": 2} | 3 | 7 | 3 | ["np.cumsum", "range", "len"] | 3 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.calibration_py.Calibration.get_calibrated_factor_for_stdev", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_tra... | The function (get_first_index) defined within the public class called public.The function start at line 17 and ends at 23. It contains 7 lines of code and it has a cyclomatic complexity of 3. It takes 2 parameters, represented as [17.0], and this function return a value. It declares 3.0 functions, It has 3.0 functions ... |
CAREamics_careamics | Calibration | public | 0 | 0 | __init__ | def __init__(self, num_bins: int = 15):self._bins = num_binsself._bin_boundaries = None | 1 | 3 | 2 | 21 | 0 | 33 | 35 | 33 | self,num_bins | [] | None | {"Assign": 2} | 0 | 3 | 0 | [] | 8,182 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.15197461_googleapis_python_cloud_core.google.cloud._helpers.__init___py._LocalStack.__init__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16798231_kapji_capital_gains_calculator.cgt_calc.exceptions_py.AmountMissi... | The function (__init__) defined within the public class called Calibration.The function start at line 33 and ends at 35. It contains 3 lines of code and it has a cyclomatic complexity of 1. It takes 2 parameters, represented as [33.0] and does not return any value. It has 8182.0 functions calling this function which ar... |
CAREamics_careamics | Calibration | public | 0 | 0 | compute_bin_boundaries | def compute_bin_boundaries(self, predict_std: np.ndarray) -> np.ndarray:"""Compute the bin boundaries for `num_bins` bins and predicted std values."""min_std = np.min(predict_std)max_std = np.max(predict_std)return np.linspace(min_std, max_std, self._bins + 1) | 1 | 4 | 2 | 47 | 0 | 37 | 41 | 37 | self,predict_std | [] | np.ndarray | {"Assign": 2, "Expr": 1, "Return": 1} | 3 | 5 | 3 | ["np.min", "np.max", "np.linspace"] | 0 | [] | The function (compute_bin_boundaries) defined within the public class called Calibration.The function start at line 37 and ends at 41. It contains 4 lines of code and it has a cyclomatic complexity of 1. It takes 2 parameters, represented as [37.0] and does not return any value. It declares 3.0 functions, and It has 3... |
CAREamics_careamics | Calibration | public | 0 | 0 | compute_stats | def compute_stats(self, pred: np.ndarray, pred_std: np.ndarray, target: np.ndarray) -> dict[int, dict[str, Union[np.ndarray, list]]]:"""It computes the bin-wise RMSE and RMV for each channel of the predicted image.Recall that:- RMSE = np.sqrt((pred - target)**2 / num_pixels)- RMV = np.sqrt(np.mean(pred_std**2))ALGORITH... | 6 | 43 | 4 | 358 | 0 | 43 | 110 | 43 | self,pred,pred_std,target | [] | dict[int, dict[str, Union[np.ndarray, list]]] | {"Assign": 20, "Expr": 5, "For": 2, "Return": 1} | 18 | 68 | 18 | ["range", "self.compute_bin_boundaries", "np.digitize", "std_ch.reshape", "bin_matrix.reshape", "range", "np.sum", "np.sqrt", "np.sum", "np.std", "np.sqrt", "np.sqrt", "np.mean", "append", "append", "append", "np.sqrt", "append"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.70179132_vyperlang_titanoboa.boa.profiling_py.get_call_profile_table"] | The function (compute_stats) defined within the public class called Calibration.The function start at line 43 and ends at 110. It contains 43 lines of code and it has a cyclomatic complexity of 6. It takes 4 parameters, represented as [43.0] and does not return any value. It declares 18.0 functions, It has 18.0 functio... |
CAREamics_careamics | Calibration | public | 0 | 0 | get_calibrated_factor_for_stdev | def get_calibrated_factor_for_stdev(self,pred: Optional[np.ndarray] = None,pred_std: Optional[np.ndarray] = None,target: Optional[np.ndarray] = None,q_s: float = 0.00001,q_e: float = 0.99999,) -> dict[str, float]:"""Calibrate the uncertainty by multiplying the predicted std with a scalar.Parameters----------stats_dict ... | 5 | 29 | 6 | 247 | 0 | 112 | 157 | 112 | self,pred,pred_std,target,q_s,q_e | [] | dict[str, float] | {"Assign": 13, "Expr": 2, "For": 1, "If": 2, "Return": 1} | 10 | 46 | 10 | ["hasattr", "print", "any", "ValueError", "self.compute_stats", "self.stats_dict.keys", "get_first_index", "get_last_index", "stats.linregress", "self.get_factors_array"] | 0 | [] | The function (get_calibrated_factor_for_stdev) defined within the public class called Calibration.The function start at line 112 and ends at 157. It contains 29 lines of code and it has a cyclomatic complexity of 5. It takes 6 parameters, represented as [112.0] and does not return any value. It declares 10.0 functions,... |
CAREamics_careamics | Calibration | public | 0 | 0 | get_factors_array | def get_factors_array(self, factors_dict: list[dict]):"""Get the calibration factors as a numpy array."""calib_scalar = [factors_dict[i]["scalar"] for i in range(len(factors_dict))]calib_scalar = np.array(calib_scalar).reshape(1, 1, 1, -1)calib_offset = [factors_dict[i].get("offset", 0.0) for i in range(len(factors_dic... | 3 | 8 | 2 | 111 | 0 | 159 | 167 | 159 | self,factors_dict | [] | Returns | {"Assign": 4, "Expr": 1, "Return": 1} | 9 | 9 | 9 | ["range", "len", "reshape", "np.array", "get", "range", "len", "reshape", "np.array"] | 0 | [] | The function (get_factors_array) defined within the public class called Calibration.The function start at line 159 and ends at 167. It contains 8 lines of code and it has a cyclomatic complexity of 3. It takes 2 parameters, represented as [159.0], and this function return a value. It declares 9.0 functions, and It has... |
CAREamics_careamics | public | public | 0 | 0 | plot_calibration | def plot_calibration(ax, calibration_stats):first_idx = get_first_index(calibration_stats[0]["bin_count"], 0.0001)last_idx = get_last_index(calibration_stats[0]["bin_count"], 0.9999)ax.plot(calibration_stats[0]["rmv"][first_idx:-last_idx],calibration_stats[0]["rmse"][first_idx:-last_idx],"o",label=r"$\hat{C}_0$: Ch1",)... | 1 | 20 | 2 | 168 | 2 | 170 | 191 | 170 | ax,calibration_stats | ['last_idx', 'first_idx'] | None | {"Assign": 4, "Expr": 5} | 9 | 22 | 9 | ["get_first_index", "get_last_index", "ax.plot", "get_first_index", "get_last_index", "ax.plot", "ax.set_xlabel", "ax.set_ylabel", "ax.legend"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.plot_crops"] | The function (plot_calibration) defined within the public class called public.The function start at line 170 and ends at 191. It contains 20 lines of code and it has a cyclomatic complexity of 1. It takes 2 parameters, represented as [170.0] and does not return any value. It declares 9.0 functions, It has 9.0 functions... |
CAREamics_careamics | public | public | 0 | 0 | clean_ax | def clean_ax(ax):"""Helper function to remove ticks from axes in plots."""# 2D or 1D axes are of type np.ndarrayif isinstance(ax, np.ndarray):for one_ax in ax:clean_ax(one_ax)returnax.set_yticklabels([])ax.set_xticklabels([])ax.tick_params(left=False, right=False, top=False, bottom=False) | 3 | 8 | 1 | 60 | 0 | 37 | 49 | 37 | ax | [] | None | {"Expr": 5, "For": 1, "If": 1, "Return": 1} | 5 | 13 | 5 | ["isinstance", "clean_ax", "ax.set_yticklabels", "ax.set_xticklabels", "ax.tick_params"] | 2 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.clean_ax", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.plot_crops"] | The function (clean_ax) defined within the public class called public.The function start at line 37 and ends at 49. It contains 8 lines of code and it has a cyclomatic complexity of 3. The function does not take any parameters and does not return any value. It declares 5.0 functions, It has 5.0 functions called inside ... |
CAREamics_careamics | public | public | 0 | 0 | get_eval_output_dir | def get_eval_output_dir(saveplotsdir: str, patch_size: int, mmse_count: int = 50) -> str:"""Given the path to a root directory to save plots, patch size, and mmse count,it returns the specific directory to save the plots."""eval_out_dir = os.path.join(saveplotsdir, f"eval_outputs/patch_{patch_size}_mmse_{mmse_count}")o... | 1 | 9 | 3 | 49 | 1 | 52 | 64 | 52 | saveplotsdir,patch_size,mmse_count | ['eval_out_dir'] | str | {"Assign": 1, "Expr": 3, "Return": 1} | 3 | 13 | 3 | ["os.path.join", "os.makedirs", "print"] | 0 | [] | The function (get_eval_output_dir) defined within the public class called public.The function start at line 52 and ends at 64. It contains 9 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [52.0] and does not return any value. It declares 3.0 functions, and It has 3.0 funct... |
CAREamics_careamics | public | public | 0 | 0 | get_psnr_str | def get_psnr_str(tar_hsnr, pred, col_idx):"""Compute PSNR between the ground truth (`tar_hsnr`) and the predicted image (`pred`)."""return f"{scale_invariant_psnr(tar_hsnr[col_idx][None], pred[col_idx][None]).item():.1f}" | 1 | 2 | 3 | 13 | 0 | 67 | 71 | 67 | tar_hsnr,pred,col_idx | [] | Returns | {"Expr": 1, "Return": 1} | 2 | 5 | 2 | ["item", "scale_invariant_psnr"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.plot_crops"] | The function (get_psnr_str) defined within the public class called public.The function start at line 67 and ends at 71. It contains 2 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [67.0], and this function return a value. It declares 2.0 functions, It has 2.0 functions cal... |
CAREamics_careamics | public | public | 0 | 0 | add_psnr_str | def add_psnr_str(ax_, psnr):"""Add psnr string to the axes"""textstr = f"PSNR\n{psnr}"props = dict(boxstyle="round", facecolor="gray", alpha=0.5)# place a text box in upper left in axes coordsax_.text(0.05,0.95,textstr,transform=ax_.transAxes,fontsize=11,verticalalignment="top",bbox=props,color="white",) | 1 | 13 | 2 | 67 | 2 | 74 | 90 | 74 | ax_,psnr | ['textstr', 'props'] | None | {"Assign": 2, "Expr": 2} | 2 | 17 | 2 | ["dict", "ax_.text"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.plot_crops"] | The function (add_psnr_str) defined within the public class called public.The function start at line 74 and ends at 90. It contains 13 lines of code and it has a cyclomatic complexity of 1. It takes 2 parameters, represented as [74.0] and does not return any value. It declares 2.0 functions, It has 2.0 functions called... |
CAREamics_careamics | public | public | 0 | 0 | get_last_index | def get_last_index(bin_count, quantile):cumsum = np.cumsum(bin_count)normalized_cumsum = cumsum / cumsum[-1]for i in range(1, len(normalized_cumsum)):if normalized_cumsum[-i] < quantile:return i - 1return None | 3 | 7 | 2 | 52 | 2 | 93 | 99 | 93 | bin_count,quantile | ['normalized_cumsum', 'cumsum'] | Returns | {"Assign": 2, "For": 1, "If": 1, "Return": 2} | 3 | 7 | 3 | ["np.cumsum", "range", "len"] | 3 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.calibration_py.Calibration.get_calibrated_factor_for_stdev", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_tra... | The function (get_last_index) defined within the public class called public.The function start at line 93 and ends at 99. It contains 7 lines of code and it has a cyclomatic complexity of 3. It takes 2 parameters, represented as [93.0], and this function return a value. It declares 3.0 functions, It has 3.0 functions c... |
CAREamics_careamics | public | public | 0 | 0 | get_first_index | def get_first_index(bin_count, quantile):cumsum = np.cumsum(bin_count)normalized_cumsum = cumsum / cumsum[-1]for i in range(len(normalized_cumsum)):if normalized_cumsum[i] > quantile:return ireturn None | 3 | 7 | 2 | 47 | 2 | 102 | 108 | 102 | bin_count,quantile | ['normalized_cumsum', 'cumsum'] | Returns | {"Assign": 2, "For": 1, "If": 1, "Return": 2} | 3 | 7 | 3 | ["np.cumsum", "range", "len"] | 3 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.calibration_py.Calibration.get_calibrated_factor_for_stdev", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_tra... | The function (get_first_index) defined within the public class called public.The function start at line 102 and ends at 108. It contains 7 lines of code and it has a cyclomatic complexity of 3. It takes 2 parameters, represented as [102.0], and this function return a value. It declares 3.0 functions, It has 3.0 functio... |
CAREamics_careamics | public | public | 0 | 0 | get_device | def get_device():if torch.cuda.is_available():return "cuda"elif torch.backends.mps.is_available():return "mps"else:return "cpu" | 3 | 7 | 0 | 32 | 0 | 111 | 117 | 111 | [] | Returns | {"If": 2, "Return": 3} | 2 | 7 | 2 | ["torch.cuda.is_available", "torch.backends.mps.is_available"] | 6 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.get_single_file_mmse", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.get_... | The function (get_device) defined within the public class called public.The function start at line 111 and ends at 117. It contains 7 lines of code and it has a cyclomatic complexity of 3. The function does not take any parameters, and this function return a value. It declares 2.0 functions, It has 2.0 functions called... | |
CAREamics_careamics | public | public | 0 | 0 | show_for_one | def show_for_one(idx,val_dset,highsnr_val_dset,model,calibration_stats,mmse_count=5,patch_size=256,num_samples=2,baseline_preds=None,):"""Given an index, it plots the input, target, reconstructed images and the difference image.Note the the difference image is computed with respect to a ground truth image, obtained fro... | 1 | 26 | 9 | 95 | 0 | 120 | 149 | 120 | idx,val_dset,highsnr_val_dset,model,calibration_stats,mmse_count,patch_size,num_samples,baseline_preds | [] | None | {"Assign": 2, "Expr": 4} | 4 | 30 | 4 | ["highsnr_val_dset.set_img_sz", "highsnr_val_dset.disable_noise", "get_predictions", "plot_crops"] | 0 | [] | The function (show_for_one) defined within the public class called public.The function start at line 120 and ends at 149. It contains 26 lines of code and it has a cyclomatic complexity of 1. It takes 9 parameters, represented as [120.0] and does not return any value. It declares 4.0 functions, and It has 4.0 function... |
CAREamics_careamics | public | public | 0 | 0 | plot_crops | def plot_crops(inp,tar,tar_hsnr,recon_img_list,calibration_stats=None,num_samples=2,baseline_preds=None,):if baseline_preds is None:baseline_preds = []if len(baseline_preds) > 0:for i in range(len(baseline_preds)):if baseline_preds[i].shape != tar_hsnr.shape:print(f"Baseline prediction {i} shape {baseline_preds[i].shap... | 15 | 130 | 7 | 904 | 25 | 152 | 354 | 152 | inp,tar,tar_hsnr,recon_img_list,calibration_stats,num_samples,baseline_preds | ['inset_rect', 'grid_img_sz', 'fig_w', 'grid_factor', 'legend_ch2_ax', 'color_pred', 'c0_extra', 'insetplot_xmax_value', 'params', 'sample_start_idx', 'example_spacing', 'fig', 'baseline_preds', 'smaller_offset', 'nimgs', 'fig_h', 'insetplot_xmin_value', 'psnr', 'gs', 'ncols', 'color_ch_list', 'legend_ch1_ax', 'ax_temp... | None | {"Assign": 34, "Expr": 22, "For": 7, "If": 7, "Return": 1} | 56 | 203 | 56 | ["len", "range", "len", "print", "print", "len", "int", "plt.figure", "GridSpec", "int", "int", "plt.rcParams.update", "range", "len", "range", "fig.add_subplot", "print", "get_psnr_str", "ax_temp.imshow", "add_psnr_str", "clean_ax", "len", "range", "range", "fig.add_subplot", "get_psnr_str", "ax_temp.imshow", "add_psn... | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.show_for_one"] | The function (plot_crops) defined within the public class called public.The function start at line 152 and ends at 354. It contains 130 lines of code and it has a cyclomatic complexity of 15. It takes 7 parameters, represented as [152.0] and does not return any value. It declares 56.0 functions, It has 56.0 functions c... |
CAREamics_careamics | public | public | 0 | 0 | plot_calibration | def plot_calibration(ax, calibration_stats):"""To plot calibration statistics (RMV vs RMSE)."""first_idx = get_first_index(calibration_stats[0]["bin_count"], 0.001)last_idx = get_last_index(calibration_stats[0]["bin_count"], 0.999)ax.plot(calibration_stats[0]["rmv"][first_idx:-last_idx],calibration_stats[0]["rmse"][fir... | 1 | 20 | 2 | 169 | 2 | 357 | 381 | 357 | ax,calibration_stats | ['last_idx', 'first_idx'] | None | {"Assign": 4, "Expr": 6} | 9 | 25 | 9 | ["get_first_index", "get_last_index", "ax.plot", "get_first_index", "get_last_index", "ax.plot", "ax.set_xlabel", "ax.set_ylabel", "ax.legend"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.plot_crops"] | The function (plot_calibration) defined within the public class called public.The function start at line 357 and ends at 381. It contains 20 lines of code and it has a cyclomatic complexity of 1. It takes 2 parameters, represented as [357.0] and does not return any value. It declares 9.0 functions, It has 9.0 functions... |
CAREamics_careamics | public | public | 0 | 0 | shiftedColorMap | def shiftedColorMap(cmap, start=0, midpoint=0.5, stop=1.0, name="shiftedcmap"):"""Adapted from https://stackoverflow.com/questions/7404116/defining-the-midpoint-of-a-colormap-in-matplotlibFunction to offset the "center" of a colormap. Useful fordata with a negative min and positive max and you want themiddle of the col... | 2 | 20 | 5 | 241 | 6 | 384 | 433 | 384 | cmap,start,midpoint,stop,name | ['newcmap', 'shift_index', 'mid_idx', 'a', 'cdict', 'reg_index'] | Returns | {"Assign": 7, "Expr": 6, "For": 1, "Return": 1} | 14 | 50 | 14 | ["np.linspace", "len", "np.hstack", "np.linspace", "np.linspace", "zip", "cmap", "np.abs", "append", "append", "append", "append", "matplotlib.colors.LinearSegmentedColormap", "matplotlib.colormaps.register"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.plot_error"] | The function (shiftedColorMap) defined within the public class called public.The function start at line 384 and ends at 433. It contains 20 lines of code and it has a cyclomatic complexity of 2. It takes 5 parameters, represented as [384.0], and this function return a value. It declares 14.0 functions, It has 14.0 func... |
CAREamics_careamics | public | public | 0 | 0 | get_fractional_change | def get_fractional_change(target, prediction, max_val=None):"""Get relative difference between target and prediction."""if max_val is None:max_val = target.max()return (target - prediction) / max_val | 2 | 4 | 3 | 32 | 1 | 436 | 442 | 436 | target,prediction,max_val | ['max_val'] | Returns | {"Assign": 1, "Expr": 1, "If": 1, "Return": 1} | 1 | 7 | 1 | ["target.max"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.plot_error"] | The function (get_fractional_change) defined within the public class called public.The function start at line 436 and ends at 442. It contains 4 lines of code and it has a cyclomatic complexity of 2. It takes 3 parameters, represented as [436.0], and this function return a value. It declare 1.0 function, It has 1.0 fun... |
CAREamics_careamics | public | public | 0 | 0 | get_zero_centered_midval | def get_zero_centered_midval(error):"""When done this way, the midval ensures that the colorbar is centered at 0. (Don't know how, but it works ;))"""vmax = error.max()vmin = error.min()midval = 1 - vmax / (vmax + abs(vmin))return midval | 1 | 5 | 1 | 36 | 3 | 445 | 452 | 445 | error | ['vmax', 'midval', 'vmin'] | Returns | {"Assign": 3, "Expr": 1, "Return": 1} | 3 | 8 | 3 | ["error.max", "error.min", "abs"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.plot_error"] | The function (get_zero_centered_midval) defined within the public class called public.The function start at line 445 and ends at 452. It contains 5 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters, and this function return a value. It declares 3.0 functions, It has 3.0 fu... |
CAREamics_careamics | public | public | 0 | 0 | plot_error | def plot_error(target, prediction, cmap=matplotlib.cm.coolwarm, ax=None, max_val=None):"""Plot the relative difference between target and prediction.NOTE: The plot is overlapped to the prediction image (in gray scale).NOTE: The colorbar is centered at 0."""if ax is None:_, ax = plt.subplots(figsize=(6, 6))# Relative di... | 2 | 11 | 5 | 123 | 4 | 455 | 472 | 455 | target,prediction,cmap,ax,max_val | ['midval', 'img_err', 'rel_diff', 'shifted_cmap'] | None | {"Assign": 5, "Expr": 3, "If": 1} | 7 | 18 | 7 | ["plt.subplots", "get_fractional_change", "get_zero_centered_midval", "shiftedColorMap", "ax.imshow", "ax.imshow", "plt.colorbar"] | 0 | [] | The function (plot_error) defined within the public class called public.The function start at line 455 and ends at 472. It contains 11 lines of code and it has a cyclomatic complexity of 2. It takes 5 parameters, represented as [455.0] and does not return any value. It declares 7.0 functions, and It has 7.0 functions ... |
CAREamics_careamics | public | public | 0 | 0 | get_predictions | def get_predictions(model: VAEModule,dset: Dataset,batch_size: int,tile_size: Optional[tuple[int, int]] = None,grid_size: Optional[int] = None,mmse_count: int = 1,num_workers: int = 4,) -> tuple[dict, dict, dict]:"""Get patch-wise predictions from a model for the entire dataset.Parameters----------model : VAEModuleLigh... | 3 | 44 | 7 | 204 | 3 | 478 | 553 | 478 | model,dset,batch_size,tile_size,grid_size,mmse_count,num_workers | ['multifile_stitched_stds', 'multifile_stitched_predictions', 'filename'] | tuple[dict, dict, dict] | {"Assign": 8, "Expr": 1, "For": 1, "If": 1, "Return": 2} | 3 | 76 | 3 | ["hasattr", "get_single_file_mmse", "get_single_file_mmse"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.show_for_one"] | The function (get_predictions) defined within the public class called public.The function start at line 478 and ends at 553. It contains 44 lines of code and it has a cyclomatic complexity of 3. It takes 7 parameters, represented as [478.0] and does not return any value. It declares 3.0 functions, It has 3.0 functions ... |
CAREamics_careamics | public | public | 0 | 0 | get_single_file_predictions | def get_single_file_predictions(model: VAEModule,dset: Dataset,batch_size: int,tile_size: Optional[tuple[int, int]] = None,grid_size: Optional[int] = None,num_workers: int = 4,) -> tuple[np.ndarray, np.ndarray]:"""Get patch-wise predictions from a model for a single file dataset."""if tile_size and grid_size:dset.set_i... | 5 | 37 | 6 | 255 | 9 | 556 | 601 | 556 | model,dset,batch_size,tile_size,grid_size,num_workers | ['device', 'dloader', 'logvar', 'tiles', 'tile_samples', 'tar', 'inp', 'rec_img', 'logvar_arr'] | tuple[np.ndarray, np.ndarray] | {"Assign": 12, "Expr": 6, "For": 1, "If": 2, "Return": 1, "With": 1} | 20 | 46 | 20 | ["dset.set_img_sz", "get_device", "DataLoader", "model.eval", "model.to", "torch.no_grad", "tqdm", "inp.to", "tar.to", "model", "torch.tensor", "torch.chunk", "logvar_arr.append", "numpy", "logvar.cpu", "tiles.append", "numpy", "rec_img.cpu", "np.concatenate", "stitch_predictions_new"] | 0 | [] | The function (get_single_file_predictions) defined within the public class called public.The function start at line 556 and ends at 601. It contains 37 lines of code and it has a cyclomatic complexity of 5. It takes 6 parameters, represented as [556.0] and does not return any value. It declares 20.0 functions, and It ... |
CAREamics_careamics | public | public | 0 | 0 | get_single_file_mmse | def get_single_file_mmse(model: VAEModule,dset: Dataset,batch_size: int,tile_size: Optional[tuple[int, int]] = None,grid_size: Optional[int] = None,mmse_count: int = 1,num_workers: int = 4,) -> tuple[np.ndarray, np.ndarray]:"""Get patch-wise predictions from a model for a single file dataset."""device = get_device()dlo... | 7 | 53 | 7 | 406 | 17 | 604 | 670 | 604 | model,dset,batch_size,tile_size,grid_size,mmse_count,num_workers | ['stitched_stds', 'inp', 'samples', 'tile_mmse', 'mmse_imgs', 'tiles_arr', 'stitch_func', 'stitched_predictions', 'device', 'rec_img_list', 'dloader', 'logvar', 'std_imgs', 'tar', 'tile_stds', 'rec_img', 'logvar_arr'] | tuple[np.ndarray, np.ndarray] | {"Assign": 22, "Expr": 8, "For": 2, "If": 3, "Return": 1, "With": 1} | 36 | 67 | 36 | ["get_device", "DataLoader", "dset.set_img_sz", "model.eval", "model.to", "torch.no_grad", "tqdm", "inp.to", "tar.to", "range", "model", "torch.tensor", "torch.chunk", "rec_img_list.append", "unsqueeze", "rec_img.cpu", "logvar_arr.append", "numpy", "logvar.cpu", "torch.cat", "torch.mean", "torch.std", "tile_mmse.append... | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.get_predictions"] | The function (get_single_file_mmse) defined within the public class called public.The function start at line 604 and ends at 670. It contains 53 lines of code and it has a cyclomatic complexity of 7. It takes 7 parameters, represented as [604.0] and does not return any value. It declares 36.0 functions, It has 36.0 fun... |
CAREamics_careamics | PatchLocation | public | 0 | 0 | __init__ | def __init__(self, h_idx_range, w_idx_range, t_idx):self.t = t_idxself.h_start, self.h_end = h_idx_rangeself.w_start, self.w_end = w_idx_range | 1 | 4 | 4 | 34 | 0 | 680 | 683 | 680 | self,h_idx_range,w_idx_range,t_idx | [] | None | {"Assign": 3} | 0 | 4 | 0 | [] | 8,182 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.15197461_googleapis_python_cloud_core.google.cloud._helpers.__init___py._LocalStack.__init__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.16798231_kapji_capital_gains_calculator.cgt_calc.exceptions_py.AmountMissi... | The function (__init__) defined within the public class called PatchLocation.The function start at line 680 and ends at 683. It contains 4 lines of code and it has a cyclomatic complexity of 1. It takes 4 parameters, represented as [680.0] and does not return any value. It has 8182.0 functions calling this function whi... |
CAREamics_careamics | PatchLocation | public | 0 | 0 | __str__ | def __str__(self):msg = f"T:{self.t} [{self.h_start}-{self.h_end}) [{self.w_start}-{self.w_end}) "return msg | 1 | 3 | 1 | 11 | 0 | 685 | 687 | 685 | self | [] | Returns | {"Assign": 1, "Return": 1} | 0 | 3 | 0 | [] | 19 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.3646959_kristianoellegaard_django_hvad.hvad.test_utils.project.app.models_py.NormalProxy.__str__", "_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.3646959_kristianoellegaard_django_hvad.hvad.test_utils.project.app.mod... | The function (__str__) defined within the public class called PatchLocation.The function start at line 685 and ends at 687. It contains 3 lines of code and it has a cyclomatic complexity of 1. The function does not take any parameters, and this function return a value. It has 19.0 functions calling this function which ... |
CAREamics_careamics | public | public | 0 | 0 | _get_location | def _get_location(extra_padding, hwt, pred_h, pred_w):h_start, w_start, t_idx = hwth_start -= extra_paddingh_end = h_start + pred_hw_start -= extra_paddingw_end = w_start + pred_wreturn PatchLocation((h_start, h_end), (w_start, w_end), t_idx) | 1 | 7 | 4 | 51 | 2 | 690 | 696 | 690 | extra_padding,hwt,pred_h,pred_w | ['h_end', 'w_end'] | Returns | {"Assign": 3, "AugAssign": 2, "Return": 1} | 1 | 7 | 1 | ["PatchLocation"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.get_location_from_idx"] | The function (_get_location) defined within the public class called public.The function start at line 690 and ends at 696. It contains 7 lines of code and it has a cyclomatic complexity of 1. It takes 4 parameters, represented as [690.0], and this function return a value. It declare 1.0 function, It has 1.0 function ca... |
CAREamics_careamics | public | public | 0 | 0 | get_location_from_idx | def get_location_from_idx(dset, dset_input_idx, pred_h, pred_w):"""For a given idx of the dataset, it returns where exactly in the dataset, does this prediction lies.Note that this prediction also has padded pixels and so a subset of it will be used in the final prediction.Which time frame, which spatial location (h_st... | 1 | 6 | 4 | 50 | 2 | 699 | 717 | 699 | dset,dset_input_idx,pred_h,pred_w | ['htw', 'extra_padding'] | Returns | {"Assign": 2, "Expr": 1, "Return": 1} | 5 | 19 | 5 | ["dset.per_side_overlap_pixelcount", "hwt_from_idx", "dset.get_idx_manager", "dset.get_grid_size", "_get_location"] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.stitch_predictions"] | The function (get_location_from_idx) defined within the public class called public.The function start at line 699 and ends at 717. It contains 6 lines of code and it has a cyclomatic complexity of 1. It takes 4 parameters, represented as [699.0], and this function return a value. It declares 5.0 functions, It has 5.0 f... |
CAREamics_careamics | public | public | 0 | 0 | remove_pad | def remove_pad(pred, loc, extra_padding, smoothening_pixelcount, frame_shape):assert smoothening_pixelcount == 0if extra_padding - smoothening_pixelcount > 0:h_s = extra_padding - smoothening_pixelcount# rowsh_N = frame_shape[0]if loc.h_end > h_N:assert loc.h_end - extra_padding + smoothening_pixelcount <= h_Nh_e = ext... | 4 | 15 | 5 | 105 | 6 | 720 | 742 | 720 | pred,loc,extra_padding,smoothening_pixelcount,frame_shape | ['w_e', 'h_s', 'h_N', 'w_s', 'h_e', 'w_N'] | Returns | {"Assign": 6, "If": 3, "Return": 2} | 0 | 23 | 0 | [] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.stitch_predictions"] | The function (remove_pad) defined within the public class called public.The function start at line 720 and ends at 742. It contains 15 lines of code and it has a cyclomatic complexity of 4. It takes 5 parameters, represented as [720.0], and this function return a value. It has 1.0 function calling this function which i... |
CAREamics_careamics | public | public | 0 | 0 | update_loc_for_final_insertion | def update_loc_for_final_insertion(loc, extra_padding, smoothening_pixelcount):extra_padding = extra_padding - smoothening_pixelcountloc.h_start += extra_paddingloc.w_start += extra_paddingloc.h_end -= extra_paddingloc.w_end -= extra_paddingreturn loc | 1 | 7 | 3 | 36 | 1 | 745 | 751 | 745 | loc,extra_padding,smoothening_pixelcount | ['extra_padding'] | Returns | {"Assign": 1, "AugAssign": 4, "Return": 1} | 0 | 7 | 0 | [] | 1 | ["_.content.gdrive.MyDrive.Phd_Thesis.Dataset_Creation.Output.Cloned_Repo_3.95053985_CAREamics_careamics.src.careamics.lvae_training.eval_utils_py.stitch_predictions"] | The function (update_loc_for_final_insertion) defined within the public class called public.The function start at line 745 and ends at 751. It contains 7 lines of code and it has a cyclomatic complexity of 1. It takes 3 parameters, represented as [745.0], and this function return a value. It has 1.0 function calling th... |
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