datamint 1.7.6__py3-none-any.whl → 1.9.0__py3-none-any.whl

datamint/apihandler/base_api_handler.py

@@ -119,9 +119,6 @@ class BaseAPIHandler:
         if method != 'GET':
             curl_command.extend(['-X', method])
 
-        # Add URL
-        curl_command.append(f"'{url}'")
-
         # Add headers
         for key, value in headers.items():
             if key.lower() == 'apikey':
@@ -132,6 +129,8 @@ class BaseAPIHandler:
         if params:
             param_str = '&'.join([f"{k}={v}" for k, v in params.items()])
             url = f"{url}?{param_str}"
+        # Add URL
+        curl_command.append(f"'{url}'")
 
         # Add data
         if data:

datamint/apihandler/root_api_handler.py

@@ -8,7 +8,7 @@ import asyncio
 import aiohttp
 from medimgkit.dicom_utils import anonymize_dicom, to_bytesio, is_dicom, is_dicom_report
 from medimgkit import dicom_utils, standardize_mimetype
-from medimgkit.io_utils import is_io_object
+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 pydicom
@@ -103,16 +103,22 @@ class RootAPIHandler(BaseAPIHandler):
         filename = os.path.basename(name)
         _LOGGER.debug(f"File name '{filename}' mimetype: {mimetype}")
 
-        if anonymize:
-            if is_a_dicom_file == True or is_dicom(file_path):
-                ds = pydicom.dcmread(file_path)
+        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)
-                # make the dicom `ds` object a file-like object in order to avoid unnecessary disk writes
-                f = to_bytesio(ds, name)
-            else:
-                _LOGGER.warning(f"File {file_path} is not a dicom file. Skipping anonymization.")
-                f = _open_io(file_path)
+            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)
 
@@ -437,7 +443,7 @@ class RootAPIHandler(BaseAPIHandler):
         if assemble_dicoms:
             files_path, assembled = self._assemble_dicoms(files_path)
             assemble_dicoms = assembled
-
+        
         if segmentation_files is not None:
             if assemble_dicoms:
                 raise NotImplementedError("Segmentation files cannot be uploaded when assembling dicoms yet.")

datamint/client_cmd_tools/datamint_upload.py

@@ -5,7 +5,7 @@ from humanize import naturalsize
 import logging
 from pathlib import Path
 import sys
-from medimgkit.dicom_utils import is_dicom
+from medimgkit.dicom_utils import is_dicom, detect_dicomdir, parse_dicomdir_files
 import fnmatch
 from typing import Generator, Optional, Any
 from collections import defaultdict
@@ -35,7 +35,7 @@ def _read_segmentation_names(segmentation_names_path: str | Path) -> dict:
     if segmentation_names_path.suffix in ['.yaml', '.yml']:
         with open(segmentation_names_path, 'r') as f:
             metadata = yaml.safe_load(f)
-    elif segmentation_names_path.suffix in ['.csv', '.tsv']:
+    elif segmentation_names_path.suffix in ['.csv', '.tsv', '.txt']:
         df = pd.read_csv(segmentation_names_path,
                          header=None,
                          index_col=0,
@@ -124,6 +124,22 @@ def walk_to_depth(path: str | Path,
                   depth: int,
                   exclude_pattern: str | None = None) -> Generator[Path, None, None]:
     path = Path(path)
+    
+    # Check for DICOMDIR first at current directory level
+    dicomdir_path = detect_dicomdir(path)
+    if dicomdir_path is not None:
+        try:
+            _USER_LOGGER.info(f"Found DICOMDIR file at {path}. Using it as authoritative source for file listing.")
+            dicom_files = parse_dicomdir_files(dicomdir_path)
+            # Yield all DICOM files from DICOMDIR and return early
+            for dicom_file in dicom_files:
+                yield dicom_file
+            return
+        except Exception as e:
+            _USER_LOGGER.warning(f"Failed to parse DICOMDIR at {path}: {e}. Falling back to directory scan.")
+            # Continue with regular directory scanning below
+    
+    # Regular directory scanning
     for child in path.iterdir():
         if _is_system_file(child):
             continue
@@ -386,6 +402,46 @@ def _collect_metadata_files(files_path: list[str], auto_detect_json: bool) -> tu
     return metadata_files, filtered_files_path
 
 
+def _get_files_from_path(path: str | Path,
+                         recursive_depth: Optional[int] = None,
+                         exclude_pattern: Optional[str] = None,
+                         include_extensions: Optional[list[str]] = None,
+                         exclude_extensions: Optional[list[str]] = None) -> list[str]:
+    """
+    Get files from a path with recursive DICOMDIR detection and parsing.
+
+    Args:
+        path: Path to search for files
+        recursive_depth: Depth for recursive search (None for no recursion, -1 for unlimited)
+        exclude_pattern: Pattern to exclude directories
+        include_extensions: File extensions to include
+        exclude_extensions: File extensions to exclude
+
+    Returns:
+        List of file paths as strings
+    """
+    path = Path(path)
+
+    if path.is_file():
+        return [str(path)]
+
+    try:
+        if recursive_depth is None:
+            recursive_depth = 0
+        elif recursive_depth < 0:
+            recursive_depth = MAX_RECURSION_LIMIT
+        else:
+            recursive_depth = min(MAX_RECURSION_LIMIT, recursive_depth)
+
+        file_paths = walk_to_depth(path, recursive_depth, exclude_pattern)
+        filtered_files = filter_files(file_paths, include_extensions, exclude_extensions)
+        return [str(f) for f in filtered_files]
+
+    except Exception as e:
+        _LOGGER.error(f'Error in recursive search: {e}')
+        raise
+
+
 def _parse_args() -> tuple[Any, list[str], Optional[list[dict]], Optional[list[str]]]:
     parser = argparse.ArgumentParser(
         description='DatamintAPI command line tool for uploading DICOM files and other resources')
@@ -433,7 +489,7 @@ def _parse_args() -> tuple[Any, list[str], Optional[list[dict]], Optional[list[s
                         required=False,
                         help='Path to a yaml or csv file containing the segmentation names.' +
                         ' If yaml, the file may contain two keys: "segmentation_names" and "class_names".'
-                        ' If csv, the file should contain the following columns:'
+                        ' If csv, the file should be in itk-snap label export format, i.e, it should contain the following columns (with no header):'
                         ' index, r, g, b, ..., name')
     parser.add_argument('--yes', action='store_true',
                         help='Automatically answer yes to all prompts')
@@ -482,18 +538,13 @@ def _parse_args() -> tuple[Any, list[str], Optional[list[dict]], Optional[list[s
             if args.recursive is not None:
                 _USER_LOGGER.warning("Recursive flag ignored. Specified path is a file.")
         else:
-            try:
-                recursive_depth = 0 if args.recursive is None else args.recursive
-                if recursive_depth < 0:
-                    recursive_depth = MAX_RECURSION_LIMIT
-                else:
-                    recursive_depth = min(MAX_RECURSION_LIMIT, recursive_depth)
-                file_path = walk_to_depth(args.path, recursive_depth, args.exclude)
-                file_path = filter_files(file_path, args.include_extensions, args.exclude_extensions)
-                file_path = list(map(str, file_path))  # from Path to str
-            except Exception as e:
-                _LOGGER.error(f'Error in recursive search: {e}')
-                raise e
+            file_path = _get_files_from_path(
+                path=args.path,
+                recursive_depth=args.recursive,
+                exclude_pattern=args.exclude,
+                include_extensions=args.include_extensions,
+                exclude_extensions=args.exclude_extensions
+            )
 
         if len(file_path) == 0:
             raise ValueError(f"No valid file was found in {args.path}")

{datamint-1.7.6.dist-info → datamint-1.9.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: datamint
-Version: 1.7.6
+Version: 1.9.0
 Summary: A library for interacting with the Datamint API, designed for efficient data management, processing and Deep Learning workflows.
 Requires-Python: >=3.10
 Classifier: Programming Language :: Python :: 3
@@ -19,7 +19,7 @@ Requires-Dist: humanize (>=4.0.0,<5.0.0)
 Requires-Dist: lazy-loader (>=0.3.0)
 Requires-Dist: lightning
 Requires-Dist: matplotlib
-Requires-Dist: medimgkit (>=0.2.2)
+Requires-Dist: medimgkit (>=0.4.4)
 Requires-Dist: nest-asyncio (>=1.0.0,<2.0.0)
 Requires-Dist: nibabel (>=4.0.0)
 Requires-Dist: numpy

{datamint-1.7.6.dist-info → datamint-1.9.0.dist-info}/RECORD

@@ -1,13 +1,13 @@
 datamint/__init__.py,sha256=7rKCCsaa4RBRTIfuHB708rai1xwDHLtkFNFJGKYG5D4,757
 datamint/apihandler/annotation_api_handler.py,sha256=ZJJD_Op8eDtGcpDZOS1DRjqyDUdD3UxvtuNJK9FaPOk,57063
 datamint/apihandler/api_handler.py,sha256=cdVSddrFCKlF_BJ81LO1aJ0OP49rssjpNEFzJ6Q7YyY,384
-datamint/apihandler/base_api_handler.py,sha256=HSMi8vN-xU0LLUEh3fgcuO7mXpMsX0wrA5nO9FVvrA4,12207
+datamint/apihandler/base_api_handler.py,sha256=GQuJS3FFjxPi-2vkJtbHeNKywoa-PWa3Qvw3NGRzxug,12206
 datamint/apihandler/dto/annotation_dto.py,sha256=qId1RK1VO7dXrvGJ7dqJ31jBQB7Z8yy5x0tLSiMxTB4,7105
 datamint/apihandler/exp_api_handler.py,sha256=hFUgUgBc5rL7odK7gTW3MnrvMY1pVfJUpUdzRNobMQE,6226
-datamint/apihandler/root_api_handler.py,sha256=03eDLFYHzaQi-cv5aonKj7j0KowGK6sU5F_TCx3tRlU,59183
+datamint/apihandler/root_api_handler.py,sha256=_vgIjqt7jb1yUkhyMez1Tg-vs4xmExby4TqWnfQG4OI,59320
 datamint/client_cmd_tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 datamint/client_cmd_tools/datamint_config.py,sha256=md7dnWrbl10lPtXKbmD9yo6onLJsajeG8Vz0ZWH1v4M,8181
-datamint/client_cmd_tools/datamint_upload.py,sha256=890USkrtaH23mNjTRYVHWce2q9jSmkUNHIP_e8fnJRM,29502
+datamint/client_cmd_tools/datamint_upload.py,sha256=J62xBDTaLxwBFWDmuXhzgbmZfPWaAZLr7CKsbqgTI7U,31389
 datamint/configs.py,sha256=Bdp6NydYwyCJ2dk19_gf_o3M2ZyQOmMHpLi8wEWNHUk,1426
 datamint/dataset/__init__.py,sha256=4PlUKSvVhdfQvvuq8jQXrkdqnot-iTTizM3aM1vgSwg,47
 datamint/dataset/annotation.py,sha256=qN1IMjdfLD2ceQ6va3l76jOXA8Vb_c-eBk1oWQu6hW0,7994
@@ -22,7 +22,7 @@ datamint/logging.yaml,sha256=a5dsATpul7QHeUHB2TjABFjWaPXBMbO--dgn8GlRqwk,483
 datamint/utils/logging_utils.py,sha256=DvoA35ATYG3JTwfXEXYawDyKRfHeCrH0a9czfkmz8kM,1851
 datamint/utils/torchmetrics.py,sha256=lwU0nOtsSWfebyp7dvjlAggaqXtj5ohSEUXOg3L0hJE,2837
 datamint/utils/visualization.py,sha256=yaUVAOHar59VrGUjpAWv5eVvQSfztFG0eP9p5Vt3l-M,4470
-datamint-1.7.6.dist-info/METADATA,sha256=xq4h5h5nYUIFRNpKleMaEkIrmuHbnLhIdJwm9ucwd8g,4100
-datamint-1.7.6.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-datamint-1.7.6.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
-datamint-1.7.6.dist-info/RECORD,,
+datamint-1.9.0.dist-info/METADATA,sha256=M1oMNcVYjTVV8tfZcxxcPFijib04QC8Zz9VBQLR7tXg,4100
+datamint-1.9.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+datamint-1.9.0.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
+datamint-1.9.0.dist-info/RECORD,,