datamint 1.9.2__py3-none-any.whl → 2.0.0__py3-none-any.whl

datamint/api/endpoints/resources_api.py

@@ -0,0 +1,1013 @@
+from typing import Any, Optional, Sequence, TypeAlias, Literal, IO
+from ..base_api import ApiConfig, BaseApi
+from ..entity_base_api import EntityBaseApi, CreatableEntityApi, DeletableEntityApi
+from .annotations_api import AnnotationsApi
+from .projects_api import ProjectsApi
+from datamint.entities.resource import Resource
+from datamint.entities.annotation import Annotation
+from datamint.exceptions import DatamintException, ResourceNotFoundError
+import httpx
+from datetime import date
+import json
+import logging
+import pydicom
+from medimgkit.dicom_utils import anonymize_dicom, to_bytesio, is_dicom, is_dicom_report, GeneratorWithLength
+from medimgkit import dicom_utils, standardize_mimetype
+from medimgkit.io_utils import is_io_object, peek
+from medimgkit.format_detection import guess_typez, guess_extension, DEFAULT_MIME_TYPE
+from medimgkit.nifti_utils import DEFAULT_NIFTI_MIME, NIFTI_MIMES
+import os
+import itertools
+from tqdm.auto import tqdm
+import asyncio
+import aiohttp
+from pathlib import Path
+import nest_asyncio  # For running asyncio in jupyter notebooks
+import cv2
+from PIL import Image
+from nibabel.filebasedimages import FileBasedImage as nib_FileBasedImage
+import io
+
+
+_LOGGER = logging.getLogger(__name__)
+_USER_LOGGER = logging.getLogger('user_logger')
+
+ResourceStatus: TypeAlias = Literal['new', 'inbox', 'published', 'archived']
+"""TypeAlias: The available resource status. Possible values: 'new', 'inbox', 'published', 'archived'.
+"""
+ResourceFields: TypeAlias = Literal['modality', 'created_by', 'published_by', 'published_on', 'filename', 'created_at']
+"""TypeAlias: The available fields to order resources. Possible values: 'modality', 'created_by', 'published_by', 'published_on', 'filename', 'created_at' (default).
+"""
+
+
+def _infinite_gen(x):
+    while True:
+        yield x
+
+
+def _open_io(file_path: str | Path | IO, mode: str = 'rb') -> IO:
+    if isinstance(file_path, str) or isinstance(file_path, Path):
+        return open(file_path, 'rb')
+    return file_path
+
+
+class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
+    """API handler for resource-related endpoints."""
+
+    def __init__(self, config: ApiConfig, client: Optional[httpx.Client] = None) -> None:
+        """Initialize the resources API handler.
+
+        Args:
+            config: API configuration containing base URL, API key, etc.
+            client: Optional HTTP client instance. If None, a new one will be created.
+        """
+        super().__init__(config, Resource, 'resources', client)
+        nest_asyncio.apply()
+        self.annotations_api = AnnotationsApi(config, client)
+        self.projects_api = ProjectsApi(config, client)
+
+    def get_list(self,
+                 status: Optional[ResourceStatus] = None,
+                 from_date: date | str | None = None,
+                 to_date: date | str | None = None,
+                 tags: Optional[Sequence[str]] = None,
+                 modality: Optional[str] = None,
+                 mimetype: Optional[str] = None,
+                 #  return_ids_only: bool = False,
+                 order_field: Optional[ResourceFields] = None,
+                 order_ascending: Optional[bool] = None,
+                 channel: Optional[str] = None,
+                 project_name: str | list[str] | None = None,
+                 filename: Optional[str] = None,
+                 limit: int | None = None
+                 ) -> Sequence[Resource]:
+        """Get resources with optional filtering.
+
+        Args:
+            status: The resource status. Possible values: 'inbox', 'published', 'archived' or None. If None, it will return all resources.
+            from_date : The start date.
+            to_date: The end date.
+            tags: The tags to filter the resources.
+            modality: The modality of the resources.
+            mimetype: The mimetype of the resources.
+            order_field: The field to order the resources. See :data:`~ResourceFields`.
+            order_ascending: Whether to order the resources in ascending order.
+            project_name: The project name or a list of project names to filter resources by project.
+                If multiple projects are provided, resources will be filtered to include only those belonging to ALL of the specified projects.
+        """
+
+        # Convert datetime objects to ISO format
+        if from_date:
+            if isinstance(from_date, str):
+                date.fromisoformat(from_date)
+            else:
+                from_date = from_date.isoformat()
+        if to_date:
+            if isinstance(to_date, str):
+                date.fromisoformat(to_date)
+            else:
+                to_date = to_date.isoformat()
+
+        # Prepare the payload
+        payload = {
+            "from": from_date,
+            "to": to_date,
+            "status": status if status is not None else "",
+            "modality": modality,
+            "mimetype": mimetype,
+            # "ids": return_ids_only,
+            "order_field": order_field,
+            "order_by_asc": order_ascending,
+            "channel_name": channel,
+            "filename": filename,
+        }
+        # remove nones from payload
+        payload = {k: v for k, v in payload.items() if v is not None}
+        if project_name is not None:
+            if isinstance(project_name, str):
+                project_name = [project_name]
+            payload["project"] = json.dumps({'items': project_name,
+                                             'filterType': 'intersection'})  # union or intersection
+
+        if tags is not None:
+            if isinstance(tags, str):
+                tags = [tags]
+            tags_filter = {
+                "items": tags,
+                "filterType": "union"
+            }
+            payload['tags'] = json.dumps(tags_filter)
+
+        return super().get_list(limit=limit, params=payload)
+
+    def get_annotations(self, resource: str | Resource) -> Sequence[Annotation]:
+        """Get annotations for a specific resource.
+
+        Args:
+            resource: The resource ID or Resource instance to fetch annotations for.
+
+        Returns:
+            A sequence of Annotation objects associated with the specified resource.
+        """
+        return self.annotations_api.get_list(resource=resource)
+
+    @staticmethod
+    def __process_files_parameter(file_path: str | Sequence[str | IO | pydicom.Dataset]
+                                  ) -> Sequence[str | IO]:
+        """
+        Process the file_path parameter to ensure it is a list of file paths or IO objects.
+        """
+        if isinstance(file_path, str) and os.path.isdir(file_path):
+            return [f'{file_path}/{f}' for f in os.listdir(file_path) if os.path.isfile(f'{file_path}/{f}')]
+
+        processed_files = []
+        for item in file_path:
+            if isinstance(item, pydicom.Dataset):
+                processed_files.append(to_bytesio(item, item.filename))
+            else:
+                processed_files.append(item)
+        return processed_files
+
+    def _assemble_dicoms(self, files_path: Sequence[str | IO],
+                         progress_bar: bool = False
+                         ) -> tuple[Sequence[str | IO], bool, Sequence[int]]:
+        """
+        Assembles DICOM files into a single file.
+
+        Args:
+            files_path: The paths to the DICOM files to assemble.
+
+        Returns:
+            A tuple containing:
+                - The paths to the assembled DICOM files.
+                - A boolean indicating if the assembly was necessary.
+                - same length as the output assembled DICOMs, mapping assembled DICOM to original DICOMs.
+        """
+        dicoms_files_path = []
+        other_files_path = []
+        dicom_original_idxs = []
+        others_original_idxs = []
+        for i, f in enumerate(files_path):
+            if is_dicom(f):
+                dicoms_files_path.append(f)
+                dicom_original_idxs.append(i)
+            else:
+                other_files_path.append(f)
+                others_original_idxs.append(i)
+
+        orig_len = len(dicoms_files_path)
+        if orig_len == 0:
+            _LOGGER.debug("No DICOM files found to assemble.")
+            return files_path, False, []
+        dicoms_files_path = dicom_utils.assemble_dicoms(dicoms_files_path,
+                                                        return_as_IO=True,
+                                                        progress_bar=progress_bar)
+
+        new_len = len(dicoms_files_path)
+        if new_len != orig_len:
+            _LOGGER.info(f"Assembled {new_len} dicom files out of {orig_len} files.")
+            mapping_idx = [None] * len(files_path)
+
+            files_path = GeneratorWithLength(itertools.chain(dicoms_files_path, other_files_path),
+                                             length=new_len + len(other_files_path))
+            assembled = True
+            for orig_idx, value in zip(dicom_original_idxs, dicoms_files_path.inverse_mapping_idx):
+                mapping_idx[orig_idx] = value
+            for i, orig_idx in enumerate(others_original_idxs):
+                mapping_idx[orig_idx] = new_len + i
+        else:
+            assembled = False
+            mapping_idx = [i for i in range(len(files_path))]
+
+        return files_path, assembled, mapping_idx
+
+    async def _upload_single_resource_async(self,
+                                            file_path: str | IO,
+                                            mimetype: Optional[str] = None,
+                                            anonymize: bool = False,
+                                            anonymize_retain_codes: Sequence[tuple] = [],
+                                            tags: list[str] = [],
+                                            mung_filename: Sequence[int] | Literal['all'] | None = None,
+                                            channel: Optional[str] = None,
+                                            session=None,
+                                            modality: Optional[str] = None,
+                                            publish: bool = False,
+                                            metadata_file: Optional[str | dict] = None,
+                                            ) -> str:
+        if is_io_object(file_path):
+            name = file_path.name
+        else:
+            name = file_path
+
+        if session is not None and not isinstance(session, aiohttp.ClientSession):
+            raise ValueError("session must be an aiohttp.ClientSession object.")
+
+        name = os.path.expanduser(os.path.normpath(name))
+        if len(Path(name).parts) == 0:
+            raise ValueError(f"File path '{name}' is not valid.")
+        name = os.path.join(*[x if x != '..' else '_' for x in Path(name).parts])
+
+        if mung_filename is not None:
+            file_parts = Path(name).parts
+            if file_parts[0] == os.path.sep:
+                file_parts = file_parts[1:]
+            if mung_filename == 'all':
+                new_file_path = '_'.join(file_parts)
+            else:
+                folder_parts = file_parts[:-1]
+                new_file_path = '_'.join([folder_parts[i-1] for i in mung_filename if i <= len(folder_parts)])
+                new_file_path += '_' + file_parts[-1]
+            name = new_file_path
+            _LOGGER.debug(f"New file path: {name}")
+
+        is_a_dicom_file = None
+        if mimetype is None:
+            mimetype_list, ext = guess_typez(file_path, use_magic=True)
+            for mime in mimetype_list:
+                if mime in NIFTI_MIMES:
+                    mimetype = DEFAULT_NIFTI_MIME
+                    break
+            else:
+                if ext == '.nii.gz' or name.lower().endswith('nii.gz'):
+                    mimetype = DEFAULT_NIFTI_MIME
+                else:
+                    mimetype = mimetype_list[-1] if mimetype_list else DEFAULT_MIME_TYPE
+
+        mimetype = standardize_mimetype(mimetype)
+        filename = os.path.basename(name)
+        _LOGGER.debug(f"File name '{filename}' mimetype: {mimetype}")
+
+        if is_a_dicom_file == True or is_dicom(file_path):
+            if tags is None:
+                tags = []
+            else:
+                tags = list(tags)
+            ds = pydicom.dcmread(file_path)
+            if anonymize:
+                _LOGGER.info(f"Anonymizing {file_path}")
+                ds = anonymize_dicom(ds, retain_codes=anonymize_retain_codes)
+            lat = dicom_utils.get_dicom_laterality(ds)
+            if lat == 'L':
+                tags.append("left")
+            elif lat == 'R':
+                tags.append("right")
+            # make the dicom `ds` object a file-like object in order to avoid unnecessary disk writes
+            f = to_bytesio(ds, name)
+        else:
+            f = _open_io(file_path)
+
+        try:
+            metadata_content = None
+            metadata_dict = None
+            if metadata_file is not None:
+                if isinstance(metadata_file, dict):
+                    # Metadata is already a dictionary
+                    metadata_dict = metadata_file
+                    metadata_content = json.dumps(metadata_dict)
+                    _LOGGER.debug("Using provided metadata dictionary")
+                else:
+                    # Metadata is a file path
+                    try:
+                        with open(metadata_file, 'r') as metadata_f:
+                            metadata_content = metadata_f.read()
+                            metadata_dict = json.loads(metadata_content)
+                    except Exception as e:
+                        _LOGGER.warning(f"Failed to read metadata file {metadata_file}: {e}")
+
+                # Extract modality from metadata if available
+                if metadata_dict is not None:
+                    metadata_dict_lower = {k.lower(): v for k, v in metadata_dict.items() if isinstance(k, str)}
+                    try:
+                        if modality is None:
+                            if 'modality' in metadata_dict_lower:
+                                modality = metadata_dict_lower['modality']
+                    except Exception as e:
+                        _LOGGER.debug(f"Failed to extract modality from metadata: {e}")
+
+            form = aiohttp.FormData()
+            file_key = 'resource'
+            form.add_field('source', 'api')
+
+            form.add_field(file_key, f, filename=filename, content_type=mimetype)
+            form.add_field('source_filepath', name)  # full path to the file
+            if mimetype is not None:
+                form.add_field('mimetype', mimetype)
+            if channel is not None:
+                form.add_field('channel', channel)
+            if modality is not None:
+                form.add_field('modality', modality)
+            form.add_field('bypass_inbox', 'true' if publish else 'false')
+            if tags is not None and len(tags) > 0:
+                # comma separated list of tags
+                form.add_field('tags', ','.join([l.strip() for l in tags]))
+
+            # Add JSON metadata if provided
+            if metadata_content is not None:
+                try:
+                    _LOGGER.debug("Adding metadata to form data")
+                    form.add_field('metadata', metadata_content, content_type='application/json')
+                except Exception as e:
+                    _LOGGER.warning(f"Failed to add metadata to form: {e}")
+
+            resp_data = await self._make_request_async_json('POST',
+                                                            endpoint=self.endpoint_base,
+                                                            data=form)
+            if 'error' in resp_data:
+                raise DatamintException(resp_data['error'])
+            _LOGGER.debug(f"Response on uploading {name}: {resp_data}")
+            return resp_data['id']
+        except Exception as e:
+            if 'name' in locals():
+                _LOGGER.error(f"Error uploading {name}: {e}")
+            else:
+                _LOGGER.error(f"Error uploading {file_path}: {e}")
+            raise
+        finally:
+            f.close()
+
+    async def _upload_resources_async(self,
+                                      files_path: Sequence[str | IO],
+                                      mimetype: Optional[str] = None,
+                                      anonymize: bool = False,
+                                      anonymize_retain_codes: Sequence[tuple] = [],
+                                      on_error: Literal['raise', 'skip'] = 'raise',
+                                      tags=None,
+                                      mung_filename: Sequence[int] | Literal['all'] | None = None,
+                                      channel: Optional[str] = None,
+                                      modality: Optional[str] = None,
+                                      publish: bool = False,
+                                      segmentation_files: Sequence[dict] | None = None,
+                                      transpose_segmentation: bool = False,
+                                      metadata_files: Sequence[str | dict | None] | None = None,
+                                      progress_bar: tqdm | None = None,
+                                      ) -> list[str]:
+        if on_error not in ['raise', 'skip']:
+            raise ValueError("on_error must be either 'raise' or 'skip'")
+
+        if segmentation_files is None:
+            segmentation_files = _infinite_gen(None)
+
+        if metadata_files is None:
+            metadata_files = _infinite_gen(None)
+
+        async with aiohttp.ClientSession() as session:
+            async def __upload_single_resource(file_path, segfiles: dict[str, list | dict],
+                                               metadata_file: str | dict | None):
+                name = file_path.name if is_io_object(file_path) else file_path
+                name = os.path.basename(name)
+                rid = await self._upload_single_resource_async(
+                    file_path=file_path,
+                    mimetype=mimetype,
+                    anonymize=anonymize,
+                    anonymize_retain_codes=anonymize_retain_codes,
+                    tags=tags,
+                    session=session,
+                    mung_filename=mung_filename,
+                    channel=channel,
+                    modality=modality,
+                    publish=publish,
+                    metadata_file=metadata_file,
+                )
+                if progress_bar:
+                    progress_bar.update(1)
+                    progress_bar.set_postfix(file=name)
+                else:
+                    _USER_LOGGER.info(f'"{name}" uploaded')
+
+                if segfiles is not None:
+                    fpaths = segfiles['files']
+                    names = segfiles.get('names', _infinite_gen(None))
+                    if isinstance(names, dict):
+                        names = _infinite_gen(names)
+                    frame_indices = segfiles.get('frame_index', _infinite_gen(None))
+                    for f, name, frame_index in tqdm(zip(fpaths, names, frame_indices),
+                                                     desc=f"Uploading segmentations for {file_path}",
+                                                     total=len(fpaths)):
+                        if f is not None:
+                            await self.annotations_api._upload_segmentations_async(
+                                rid,
+                                file_path=f,
+                                name=name,
+                                frame_index=frame_index,
+                                transpose_segmentation=transpose_segmentation
+                            )
+                return rid
+
+            tasks = [__upload_single_resource(f, segfiles, metadata_file)
+                     for f, segfiles, metadata_file in zip(files_path, segmentation_files, metadata_files)]
+            return await asyncio.gather(*tasks, return_exceptions=on_error == 'skip')
+
+    def upload_resources(self,
+                         files_path: Sequence[str | IO | pydicom.Dataset],
+                         mimetype: str | None = None,
+                         anonymize: bool = False,
+                         anonymize_retain_codes: Sequence[tuple] = [],
+                         on_error: Literal['raise', 'skip'] = 'raise',
+                         tags: Sequence[str] | None = None,
+                         mung_filename: Sequence[int] | Literal['all'] | None = None,
+                         channel: str | None = None,
+                         publish: bool = False,
+                         publish_to: str | None = None,
+                         segmentation_files: Sequence[Sequence[str] | dict] | None = None,
+                         transpose_segmentation: bool = False,
+                         modality: str | None = None,
+                         assemble_dicoms: bool = True,
+                         metadata: Sequence[str | dict | None] | None = None,
+                         discard_dicom_reports: bool = True,
+                         progress_bar: bool = False
+                         ) -> Sequence[str | Exception]:
+        """
+        Upload multiple resources.
+
+        Note: For uploading a single resource, use `upload_resource()` instead.
+
+        Args:
+            files_path: A sequence of paths to resource files, IO objects, or pydicom.Dataset objects.
+                Must contain at least 2 items. Supports mixed types within the sequence.
+            mimetype (str): The mimetype of the resources. If None, it will be guessed.
+            anonymize (bool): Whether to anonymize the dicoms or not.
+            anonymize_retain_codes (Sequence[tuple]): The tags to retain when anonymizing the dicoms.
+            on_error (Literal['raise', 'skip']): Whether to raise an exception when an error occurs or to skip the error.
+            tags (Optional[Sequence[str]]): The tags to add to the resources.
+            mung_filename (Sequence[int] | Literal['all']): The parts of the filepath to keep when renaming the resource file.
+                ''all'' keeps all parts.
+            channel (Optional[str]): The channel to upload the resources to. An arbitrary name to group the resources.
+            publish (bool): Whether to directly publish the resources or not. They will have the 'published' status.
+            publish_to (Optional[str]): The project name or id to publish the resources to.
+                They will have the 'published' status and will be added to the project.
+                If this is set, `publish` parameter is ignored.
+            segmentation_files (Optional[list[Union[list[str], dict]]]): The segmentation files to upload.
+                If each element is a dict, it should have two keys: 'files' and 'names'.
+                    - files: A list of paths to the segmentation files. Example: ['seg1.nii.gz', 'seg2.nii.gz'].
+                    - names: Can be a list (same size of `files`) of labels for the segmentation files. Example: ['Brain', 'Lung']. 
+            transpose_segmentation (bool): Whether to transpose the segmentation files or not.
+            modality (Optional[str]): The modality of the resources.
+            assemble_dicoms (bool): Whether to assemble the dicom files or not based on the SeriesInstanceUID and InstanceNumber attributes.
+            metadata (Optional[list[str | dict | None]]): JSON metadata to include with each resource.
+                Must have the same length as `files_path`.
+                Can be file paths (str) or already loaded dictionaries (dict).
+
+        Raises:
+            ValueError: If a single resource is provided instead of multiple resources.
+            ResourceNotFoundError: If `publish_to` is supplied, and the project does not exists.
+
+        Returns:
+            list[str | Exception]: A list of resource IDs or errors.
+        """
+
+        if on_error not in ['raise', 'skip']:
+            raise ValueError("on_error must be either 'raise' or 'skip'")
+
+        # Check if single resource provided and raise error (list of 1 item is allowed)
+        if isinstance(files_path, IO) or isinstance(files_path, pydicom.Dataset) or (isinstance(files_path, str) and not os.path.isdir(files_path)):
+            raise ValueError(
+                "upload_resources() only accepts multiple resources. For single resource upload, use upload_resource() instead.")
+
+        files_path = ResourcesApi.__process_files_parameter(files_path)
+
+        # Discard DICOM reports
+        if discard_dicom_reports:
+            old_size = len(files_path)
+            # Create filtered lists maintaining index correspondence
+            filtered_files = []
+            filtered_metadata = []
+
+            for i, f in enumerate(files_path):
+                if not is_dicom_report(f):
+                    filtered_files.append(f)
+                    if metadata is not None:
+                        filtered_metadata.append(metadata[i])
+
+            files_path = filtered_files
+            if metadata is not None:
+                metadata = filtered_metadata
+
+            if old_size is not None and old_size != len(files_path):
+                _LOGGER.info(f"Discarded {old_size - len(files_path)} DICOM report files from upload.")
+
+        if isinstance(metadata, (str, dict)):
+            _LOGGER.debug("Converting metadatas to a list")
+            metadata = [metadata]
+
+        if metadata is not None and len(metadata) != len(files_path):
+            raise ValueError("The number of metadata files must match the number of resources.")
+        if assemble_dicoms:
+            files_path, assembled, mapping_idx = self._assemble_dicoms(files_path, progress_bar=progress_bar)
+            assemble_dicoms = assembled
+        else:
+            mapping_idx = [i for i in range(len(files_path))]
+        n_files = len(files_path)
+
+        if n_files <= 1:
+            # Disable progress bar for single file uploads
+            progress_bar = False
+
+        if segmentation_files is not None:
+            if assemble_dicoms:
+                raise NotImplementedError("Segmentation files cannot be uploaded when assembling dicoms yet.")
+            if len(segmentation_files) != len(files_path):
+                raise ValueError("The number of segmentation files must match the number of resources.")
+            else:
+                if isinstance(segmentation_files, list) and isinstance(segmentation_files[0], list):
+                    raise ValueError("segmentation_files should not be a list of lists if files_path is not a list.")
+                if isinstance(segmentation_files, dict):
+                    segmentation_files = [segmentation_files]
+
+            segmentation_files = [segfiles if (isinstance(segfiles, dict) or segfiles is None) else {'files': segfiles}
+                                  for segfiles in segmentation_files]
+
+            for segfiles in segmentation_files:
+                if segfiles is None:
+                    continue
+                if 'files' not in segfiles:
+                    raise ValueError("segmentation_files must contain a 'files' key with a list of file paths.")
+                if 'names' in segfiles:
+                    # same length as files
+                    if isinstance(segfiles['names'], (list, tuple)) and len(segfiles['names']) != len(segfiles['files']):
+                        raise ValueError(
+                            "segmentation_files['names'] must have the same length as segmentation_files['files'].")
+
+        loop = asyncio.get_event_loop()
+        pbar = None
+        try:
+            if progress_bar:
+                pbar = tqdm(total=n_files, desc="Uploading resources", unit="file")
+
+            task = self._upload_resources_async(files_path=files_path,
+                                                mimetype=mimetype,
+                                                anonymize=anonymize,
+                                                anonymize_retain_codes=anonymize_retain_codes,
+                                                on_error=on_error,
+                                                tags=tags,
+                                                mung_filename=mung_filename,
+                                                channel=channel,
+                                                publish=publish,
+                                                segmentation_files=segmentation_files,
+                                                transpose_segmentation=transpose_segmentation,
+                                                modality=modality,
+                                                metadata_files=metadata,
+                                                progress_bar=pbar
+                                                )
+
+            resource_ids = loop.run_until_complete(task)
+        finally:
+            if pbar:
+                pbar.close()
+
+        _LOGGER.info(f"Resources uploaded: {resource_ids}")
+
+        if publish_to is not None:
+            _USER_LOGGER.info('Adding resources to project')
+            resource_ids_succ = [rid for rid in resource_ids if not isinstance(rid, Exception)]
+            try:
+                self.projects_api.add_resources(resource_ids_succ, publish_to)
+            except Exception as e:
+                _LOGGER.error(f"Error adding resources to project: {e}")
+                if on_error == 'raise':
+                    raise e
+
+        if mapping_idx:
+            _LOGGER.debug(f"Mapping indices for DICOM files: {mapping_idx}")
+            resource_ids = [resource_ids[idx] for idx in mapping_idx]
+
+        return resource_ids
+
+    def upload_resource(self,
+                        file_path: str | IO | pydicom.Dataset,
+                        mimetype: str | None = None,
+                        anonymize: bool = False,
+                        anonymize_retain_codes: Sequence[tuple] = [],
+                        tags: Sequence[str] | None = None,
+                        mung_filename: Sequence[int] | Literal['all'] | None = None,
+                        channel: str | None = None,
+                        publish: bool = False,
+                        publish_to: str | None = None,
+                        segmentation_files: dict | None = None,
+                        transpose_segmentation: bool = False,
+                        modality: str | None = None,
+                        metadata: dict | str | None = None,
+                        discard_dicom_reports: bool = True
+                        ) -> str:
+        """
+        Upload a single resource.
+
+        This is a convenience method that wraps upload_resources for single file uploads.
+        It provides a cleaner interface when uploading just one file.
+
+        Args:
+            file_path: The path to the resource file or IO object.
+            mimetype: The mimetype of the resource. If None, it will be guessed.
+            anonymize: Whether to anonymize the DICOM or not.
+            anonymize_retain_codes: The tags to retain when anonymizing the DICOM.
+            tags: The tags to add to the resource.
+            mung_filename: The parts of the filepath to keep when renaming the resource file.
+                'all' keeps all parts.
+            channel: The channel to upload the resource to. An arbitrary name to group the resources.
+            publish: Whether to directly publish the resource or not. It will have the 'published' status.
+            publish_to: The project name or id to publish the resource to.
+                It will have the 'published' status and will be added to the project.
+                If this is set, `publish` parameter is ignored.
+            segmentation_files: The segmentation files to upload. Should be a dict with:
+                - 'files': A list of paths to the segmentation files. Example: ['seg1.nii.gz', 'seg2.nii.gz'].
+                - 'names': A dict mapping pixel values to class names. Example: {1: 'Brain', 2: 'Lung'}.
+            transpose_segmentation: Whether to transpose the segmentation files or not.
+            modality: The modality of the resource.
+            metadata: JSON metadata to include with the resource.
+                Can be a file path (str) or already loaded dictionary (dict).
+            discard_dicom_reports: Whether to discard DICOM reports or not.
+
+        Returns:
+            str: The resource ID of the uploaded resource.
+
+        Raises:
+            ResourceNotFoundError: If `publish_to` is supplied, and the project does not exist.
+            DatamintException: If the upload fails.
+
+        Example:
+            .. code-block:: python
+
+                # Simple upload
+                resource_id = api.resources.upload_resource('path/to/file.dcm')
+
+                # Upload with metadata and segmentation
+                resource_id = api.resources.upload_resource(
+                    'path/to/file.dcm',
+                    tags=['tutorial', 'case1'],
+                    channel='study_channel',
+                    segmentation_files={
+                        'files': ['path/to/segmentation.nii.gz'],
+                        'names': {1: 'Bone', 2: 'Tissue'}
+                    },
+                    metadata={'patient_age': 45, 'modality': 'CT'}
+                )
+        """
+        # Convert segmentation_files to the format expected by upload_resources
+        segmentation_files_list: Optional[list[list[str] | dict]] = None
+        if segmentation_files is not None:
+            segmentation_files_list = [segmentation_files]
+
+        # Call upload_resources with single file
+        result = self.upload_resources(
+            files_path=[file_path],
+            mimetype=mimetype,
+            anonymize=anonymize,
+            anonymize_retain_codes=anonymize_retain_codes,
+            tags=tags,
+            mung_filename=mung_filename,
+            channel=channel,
+            publish=publish,
+            publish_to=publish_to,
+            segmentation_files=segmentation_files_list,
+            transpose_segmentation=transpose_segmentation,
+            modality=modality,
+            metadata=[metadata],
+            discard_dicom_reports=discard_dicom_reports,
+            assemble_dicoms=False,  # No need to assemble for single file
+            progress_bar=False  # Disable progress bar for single uploads
+        )
+
+        # upload_resources returns a list, so we extract the first element
+        if isinstance(result, Sequence) and len(result) == 1:
+            r = result[0]
+            if isinstance(r, Exception):
+                raise r
+            return r
+        else:
+            # This should not happen with single file uploads, but handle it just in case
+            raise DatamintException(f"Unexpected return from upload_resources: {type(result)} | {result}")
+
+    def _determine_mimetype(self,
+                            content,
+                            resource: str | Resource) -> tuple[str | None, str | None]:
+        # Determine mimetype from file content
+        mimetype_list, ext = guess_typez(content, use_magic=True)
+        mimetype = mimetype_list[-1]
+
+        # get mimetype from resource info if not detected
+        if mimetype is None or mimetype == DEFAULT_MIME_TYPE:
+            if not isinstance(resource, Resource):
+                resource = self.get_by_id(resource)
+            mimetype = resource.mimetype or mimetype
+
+        return mimetype, ext
+
+    async def _async_download_file(self,
+                                   resource: str | Resource,
+                                   save_path: str | Path,
+                                   session: aiohttp.ClientSession | None = None,
+                                   progress_bar: tqdm | None = None,
+                                   add_extension: bool = False) -> str:
+        """
+        Asynchronously download a file from the server.
+
+        Args:
+            resource: The resource unique id or Resource object.
+            save_path: The path to save the file.
+            session: The aiohttp session to use for the request.
+            progress_bar: Optional progress bar to update after download completion.
+            add_extension: Whether to add the appropriate file extension based on content type.
+
+        Returns:
+            str: The actual path where the file was saved (important when add_extension=True).
+        """
+        save_path = str(save_path)  # Ensure save_path is a string for file operations
+        resource_id = self._entid(resource)
+        try:
+            async with self._make_request_async('GET',
+                                                f'{self.endpoint_base}/{resource_id}/file',
+                                                session=session,
+                                                headers={'accept': 'application/octet-stream'}) as resp:
+                data_bytes = await resp.read()
+
+            final_save_path = save_path
+            if add_extension:
+                # Save to temporary file first to determine mimetype from content
+                temp_path = f"{save_path}.tmp"
+                with open(temp_path, 'wb') as f:
+                    f.write(data_bytes)
+
+                # Determine mimetype from file content
+                mimetype, ext = self._determine_mimetype(content=data_bytes,
+                                                         resource=resource)
+
+                # Generate final path with extension if needed
+                if mimetype is not None and mimetype != DEFAULT_MIME_TYPE:
+                    if ext is None:
+                        ext = guess_extension(mimetype)
+                    if ext is not None and not save_path.endswith(ext):
+                        final_save_path = save_path + ext
+
+                # Move file to final location
+                os.rename(temp_path, final_save_path)
+            else:
+                # Standard save without extension detection
+                with open(final_save_path, 'wb') as f:
+                    f.write(data_bytes)
+
+            if progress_bar:
+                progress_bar.update(1)
+
+            return final_save_path
+
+        except ResourceNotFoundError as e:
+            e.set_params('resource', {'resource_id': resource_id})
+            raise e
+
+    def download_multiple_resources(self,
+                                    resources: Sequence[str] | Sequence[Resource],
+                                    save_path: Sequence[str] | str,
+                                    add_extension: bool = False,
+                                    overwrite: bool = True
+                                    ) -> list[str]:
+        """
+        Download multiple resources and save them to the specified paths.
+        This is faster than downloading them one by one.
+
+        Args:
+            resources: A list of resource unique ids.
+            save_path : A list of paths to save the files or a directory path, of same length as resources.
+                If a directory path is provided, files will be saved in that directory.
+            add_extension: Whether to add the appropriate file extension to the save_path based on the content type.
+
+        Returns:
+            list[str]: A list of paths where the files were saved. Important if `add_extension=True`.
+        """
+        if isinstance(resources, str):
+            raise ValueError("resources must be a list of resources")
+
+        async def _download_all_async():
+            async with aiohttp.ClientSession() as session:
+                tasks = [
+                    self._async_download_file(
+                        resource=r,
+                        save_path=path,
+                        session=session,
+                        progress_bar=progress_bar,
+                        add_extension=add_extension
+                    )
+                    for r, path in zip(resources, save_path)
+                ]
+                return await asyncio.gather(*tasks)
+
+        if isinstance(save_path, str):
+            save_path = [os.path.join(save_path, self._entid(r)) for r in resources]
+
+        if len(save_path) != len(resources):
+            raise ValueError("The number of save paths must match the number of resources.")
+
+        if not overwrite:
+            new_resources = []
+            new_save_path = []
+            for i in range(len(resources)):
+                if not os.path.exists(save_path[i]):
+                    new_resources.append(resources[i])
+                    new_save_path.append(save_path[i])
+            resources = new_resources
+            save_path = new_save_path
+
+        with tqdm(total=len(resources), desc="Downloading resources", unit="file") as progress_bar:
+            loop = asyncio.get_event_loop()
+            final_save_paths = loop.run_until_complete(_download_all_async())
+
+        return final_save_paths
+
+    def download_resource_file(self,
+                               resource: str | Resource,
+                               save_path: Optional[str] = None,
+                               auto_convert: bool = True,
+                               add_extension: bool = False
+                               ) -> bytes | pydicom.Dataset | Image.Image | cv2.VideoCapture | nib_FileBasedImage | tuple[Any, str]:
+        """
+        Download a resource file.
+
+        Args:
+            resource: The resource unique id or Resource instance.
+            save_path: The path to save the file.
+            auto_convert: Whether to convert the file to a known format or not.
+            add_extension: Whether to add the appropriate file extension to the save_path based on the content type.
+
+        Returns:
+            The resource content in bytes (if `auto_convert=False`) or the resource object (if `auto_convert=True`).
+            if `add_extension=True`, the function will return a tuple of (resource_data, save_path).
+
+        Raises:
+            ResourceNotFoundError: If the resource does not exists.
+
+        Example:
+            >>> api_handler.download_resource_file('resource_id', auto_convert=False)
+                returns the resource content in bytes.
+            >>> api_handler.download_resource_file('resource_id', auto_convert=True)
+                Assuming this resource is a dicom file, it will return a pydicom.Dataset object. 
+            >>> api_handler.download_resource_file('resource_id', save_path='path/to/dicomfile.dcm')
+                saves the file in the specified path.
+        """
+        if save_path is None and add_extension:
+            raise ValueError("If add_extension is True, save_path must be provided.")
+
+        try:
+            response = self._make_entity_request('GET',
+                                                 resource,
+                                                 add_path='file',
+                                                 headers={'accept': 'application/octet-stream'})
+
+            # Get mimetype if needed for auto_convert or add_extension
+            mimetype = None
+            ext = None
+            if auto_convert or add_extension:
+                mimetype, ext = self._determine_mimetype(content=response.content,
+                                                         resource=resource)
+            if auto_convert:
+                if mimetype is None:
+                    _LOGGER.warning("Could not determine mimetype. Returning a bytes array.")
+                    resource_file = response.content
+                else:
+                    try:
+                        resource_file = BaseApi.convert_format(response.content,
+                                                               mimetype,
+                                                               save_path)
+                    except ValueError as e:
+                        _LOGGER.warning(f"Could not convert file to a known format: {e}")
+                        resource_file = response.content
+                    except NotImplementedError as e:
+                        _LOGGER.warning(f"Conversion not implemented yet for {mimetype} and save_path=None." +
+                                        " Returning a bytes array. If you want the conversion for this mimetype, provide a save_path.")
+                        resource_file = response.content
+            else:
+                resource_file = response.content
+        except ResourceNotFoundError as e:
+            e.set_params('resource', {'resource_id': self._entid(resource)})
+            raise e
+
+        if save_path is not None:
+            if add_extension and mimetype is not None:
+                if ext is None:
+                    ext = guess_extension(mimetype)
+                if ext is not None and not save_path.endswith(ext):
+                    save_path += ext
+            with open(save_path, 'wb') as f:
+                f.write(response.content)
+
+            if add_extension:
+                return resource_file, save_path
+        return resource_file
+
+    def download_resource_frame(self,
+                                resource: str | Resource,
+                                frame_index: int) -> Image.Image:
+        """
+        Download a frame of a resource.
+        This is faster than downloading the whole resource and then extracting the frame.
+
+        Args:
+            resource: The resource unique id or Resource object.
+            frame_index: The index of the frame to download.
+
+        Returns:
+            Image.Image: The frame as a PIL image.
+
+        Raises:
+            ResourceNotFoundError: If the resource does not exists.
+            DatamintException: If the resource is not a video or dicom.
+        """
+        # check if the resource is an single frame image (png,jpeg,...) first.
+        # If so, download the whole resource file and return the image.
+        if not isinstance(resource, Resource):
+            resource = self.get_by_id(resource)
+        if resource.mimetype.startswith('image/') or resource.storage == 'ImageResource':
+            if frame_index != 0:
+                raise DatamintException(f"Resource {resource.id} is a single frame image, "
+                                        f"but frame_index is {frame_index}.")
+            return self.download_resource_file(resource, auto_convert=True)
+
+        try:
+            response = self._make_entity_request('GET',
+                                                 resource,
+                                                 add_path=f'frames/{frame_index}',
+                                                 headers={'accept': 'image/*'})
+            if response.status_code == 200:
+                return Image.open(io.BytesIO(response.content))
+            else:
+                raise DatamintException(
+                    f"Error downloading frame {frame_index} of resource {self._entid(resource)}: {response.text}")
+        except ResourceNotFoundError as e:
+            e.set_params('resource', {'resource_id': self._entid(resource)})
+            raise e
+
+    def publish_resources(self,
+                          resources: str | Resource | Sequence[str | Resource]) -> None:
+        """
+        Publish resources, changing their status to 'published'.
+
+        Args:
+            resources: The resources to publish. Can be a Resource object (instead of a list)
+
+        Raises:
+            ResourceNotFoundError: If the resource does not exists or the project does not exists.
+        """
+        if isinstance(resources, (Resource, str)):
+            resources = [resources]
+
+        for resource in resources:
+            try:
+                self._make_entity_request('POST', resource, add_path='publish')
+            except ResourceNotFoundError as e:
+                e.set_params('resource', {'resource_id': self._entid(resource)})
+                raise
+            except httpx.HTTPError as e:
+                if BaseApi._has_status_code(e, 400) and 'Resource must be in inbox status to be approved' in e.response.text:
+                    _LOGGER.warning(f"Resource {resource} is not in inbox status. Skipping publishing")
+                else:
+                    raise
+
+    def set_tags(self,
+                 resource: str | Resource,
+                 tags: Sequence[str],
+                 ):
+        data = {'tags': tags}
+        resource_id = self._entid(resource)
+
+        response = self._make_entity_request('PUT',
+                                             resource_id,
+                                             add_path='tags',
+                                             json=data)
+        return response