ngio 0.4.0a2__py3-none-any.whl → 0.4.0a3__py3-none-any.whl

ngio/common/_roi.py

@@ -49,7 +49,7 @@ T = TypeVar("T", int, float)
 class GenericRoi(BaseModel, Generic[T]):
     """A generic Region of Interest (ROI) model."""
 
-    name: str
+    name: str | None
     x: T
     y: T
     z: T | None = None
@@ -67,6 +67,38 @@ class GenericRoi(BaseModel, Generic[T]):
         """Calculate the intersection of this ROI with another ROI."""
         return roi_intersection(self, other)
 
+    def _nice_str(self) -> str:
+        if self.t is not None:
+            t_str = f"t={self.t}->{self.t_length}"
+        else:
+            t_str = "t=None"
+        if self.z is not None:
+            z_str = f"z={self.z}->{self.z_length}"
+        else:
+            z_str = "z=None"
+
+        y_str = f"y={self.y}->{self.y_length}"
+        x_str = f"x={self.x}->{self.x_length}"
+
+        if self.label is not None:
+            label_str = f", label={self.label}"
+        else:
+            label_str = ""
+        cls_name = self.__class__.__name__
+        return f"{cls_name}({t_str}, {z_str}, {y_str}, {x_str}{label_str})"
+
+    def get_name(self) -> str:
+        """Get the name of the ROI, or a default if not set."""
+        if self.name is not None:
+            return self.name
+        return self._nice_str()
+
+    def __repr__(self) -> str:
+        return self._nice_str()
+
+    def __str__(self) -> str:
+        return self._nice_str()
+
 
 def _1d_intersection(
     a: T | None, a_length: T | None, b: T | None, b_length: T | None
@@ -113,11 +145,17 @@ def roi_intersection(
     x, x_length = _1d_intersection(
         ref_roi.x, ref_roi.x_length, other_roi.x, other_roi.x_length
     )
+    if x is None and x_length is None:
+        # No intersection
+        return None
     assert x is not None and x_length is not None
 
     y, y_length = _1d_intersection(
         ref_roi.y, ref_roi.y_length, other_roi.y, other_roi.y_length
     )
+    if y is None and y_length is None:
+        # No intersection
+        return None
     assert y is not None and y_length is not None
 
     z, z_length = _1d_intersection(
@@ -127,11 +165,8 @@ def roi_intersection(
         ref_roi.t, ref_roi.t_length, other_roi.t, other_roi.t_length
     )
 
-    if (
-        x_length <= 0
-        or y_length <= 0
-        or (z_length is not None and z_length <= 0)
-        or (t_length is not None and t_length <= 0)
+    if (z_length is not None and z_length <= 0) or (
+        t_length is not None and t_length <= 0
     ):
         # No intersection
         return None
@@ -144,9 +179,14 @@ def roi_intersection(
             )
     label = ref_roi.label or other_roi.label
 
+    if ref_roi.name is not None and other_roi.name is not None:
+        name = f"{ref_roi.name}:{other_roi.name}"
+    else:
+        name = ref_roi.name or other_roi.name
+
     cls_ref = ref_roi.__class__
     return cls_ref(
-        name=f"[{ref_roi.name}_x_{other_roi.name}]",
+        name=name,
         x=x,
         y=y,
         z=z,

ngio/experimental/iterators/_feature.py

@@ -47,7 +47,7 @@ class FeatureExtractorIterator(AbstractIteratorBuilder):
         self._input = input_image
         self._input_label = input_label
         self._ref_image = input_image
-        self._rois = input_image.build_image_roi_table().rois()
+        self._rois = input_image.build_image_roi_table(name=None).rois()
 
         # Set iteration parameters
         self._input_slicing_kwargs = add_channel_selection_to_slicing_dict(

ngio/experimental/iterators/_image_processing.py

@@ -53,7 +53,7 @@ class ImageProcessingIterator(AbstractIteratorBuilder):
         self._input = input_image
         self._output = output_image
         self._ref_image = input_image
-        self._rois = input_image.build_image_roi_table().rois()
+        self._rois = input_image.build_image_roi_table(name=None).rois()
 
         # Set iteration parameters
         self._input_slicing_kwargs = add_channel_selection_to_slicing_dict(

ngio/experimental/iterators/_rois_utils.py

@@ -24,7 +24,7 @@ def grid(
     stride_y: int | None = None,
     stride_z: int | None = None,
     stride_t: int | None = None,
-    base_name: str = "",
+    base_name: str | None = None,
 ) -> list[Roi]:
     """This method is a placeholder for creating a regular grid of ROIs."""
     t_dim = ref_image.dimensions.get("t", default=1)
@@ -49,7 +49,7 @@ def grid(
             for y in range(0, y_dim, stride_y):
                 for x in range(0, x_dim, stride_x):
                     roi = RoiPixels(
-                        name=f"{base_name}({t}, {z}, {y}, {x})",
+                        name=base_name,
                         x=x,
                         y=y,
                         z=z,

ngio/experimental/iterators/_segmentation.py

@@ -55,7 +55,7 @@ class SegmentationIterator(AbstractIteratorBuilder):
         self._input = input_image
         self._output = output_label
         self._ref_image = input_image
-        self._rois = input_image.build_image_roi_table().rois()
+        self._rois = input_image.build_image_roi_table(name=None).rois()
 
         # Set iteration parameters
         self._input_slicing_kwargs = add_channel_selection_to_slicing_dict(

ngio/images/_abstract_image.py

@@ -445,7 +445,7 @@ class AbstractImage(Generic[_image_handler]):
         """
         consolidate_image(image=self, order=order, mode=mode)
 
-    def build_image_roi_table(self, name: str = "image") -> RoiTable:
+    def build_image_roi_table(self, name: str | None = "image") -> RoiTable:
         """Build the ROI table for an image."""
         return build_image_roi_table(image=self, name=name)
 
@@ -467,7 +467,7 @@ def consolidate_image(
     )
 
 
-def build_image_roi_table(image: AbstractImage, name: str = "image") -> RoiTable:
+def build_image_roi_table(image: AbstractImage, name: str | None = "image") -> RoiTable:
     """Build the ROI table for an image."""
     dim_x = image.dimensions.get("x")
     dim_y = image.dimensions.get("y")

ngio/images/_ome_zarr_container.py

@@ -589,7 +589,7 @@ class OmeZarrContainer:
             backend=backend,
         )
 
-    def build_image_roi_table(self, name: str = "image") -> RoiTable:
+    def build_image_roi_table(self, name: str | None = "image") -> RoiTable:
         """Compute the ROI table for an image."""
         return self.get_image().build_image_roi_table(name=name)
 

ngio/tables/v1/_roi_table.py

@@ -6,6 +6,7 @@ https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
 
 from collections.abc import Iterable
 from typing import Literal
+from uuid import uuid4
 
 import pandas as pd
 from pydantic import BaseModel
@@ -146,7 +147,7 @@ def _rois_to_dataframe(rois: dict[str, Roi], index_key: str | None) -> pd.DataFr
         len_z_micrometer = roi.z_length if roi.z_length is not None else 1.0
 
         row = {
-            index_key: roi.name,
+            index_key: roi.get_name(),
             "x_micrometer": roi.x,
             "y_micrometer": roi.y,
             "z_micrometer": z_micrometer,
@@ -179,8 +180,15 @@ class RoiDictWrapper:
     """A wrapper for a dictionary of ROIs to provide a consistent interface."""
 
     def __init__(self, rois: Iterable[Roi]) -> None:
-        self._rois_by_name = {roi.name: roi for roi in rois}
-        self._rois_by_label = {roi.label: roi for roi in rois if roi.label is not None}
+        self._rois_by_name = {}
+        self._rois_by_label = {}
+        for roi in rois:
+            name = roi.get_name()
+            if name in self._rois_by_name:
+                name = f"{name}_{uuid4().hex[:8]}"
+            self._rois_by_name[name] = roi
+            if roi.label is not None:
+                self._rois_by_label[roi.label] = roi
 
     def get_by_name(self, name: str, default: Roi | None = None) -> Roi | None:
         """Get an ROI by its name."""

{ngio-0.4.0a2.dist-info → ngio-0.4.0a3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.4.0a2
+Version: 0.4.0a3
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio

{ngio-0.4.0a2.dist-info → ngio-0.4.0a3.dist-info}/RECORD

@@ -5,7 +5,7 @@ ngio/common/_array_io_utils.py,sha256=LktLM2_2LkjYkwzyJXHZ0LyuwrQN4GYTqgpByBxNml
 ngio/common/_dimensions.py,sha256=ubBSmnQmZOmen1jUn3LWZlNXCjUuV9FTjZWzUYidOwk,4852
 ngio/common/_masking_roi.py,sha256=ZZTXordEZoq_ADk0OzADvq-5dPOwUBSuNobzFR8fpTw,5697
 ngio/common/_pyramid.py,sha256=ElY_nBcchN3eeD9obLZ31IIo42HVlDn8R-legQpNxzQ,7503
-ngio/common/_roi.py,sha256=SJ_YJx5hR35T_OIx7ev9Y-rXInu7B4VEh8VKgcsdkcg,21166
+ngio/common/_roi.py,sha256=x5HHudELvYjOmoLJulk2cNrgfOZ0o1Q1OFtldZAKIKU,22360
 ngio/common/_synt_images_utils.py,sha256=B6uYOW1NyrM06YMR-csca3_YnAAkPRTbvnbLdy9tk9E,3188
 ngio/common/_zoom.py,sha256=p_trkLLrNM6hYvchJQJOHfYpzSlzzdDJmcyTx6K5J1M,6030
 ngio/common/transforms/__init__.py,sha256=Dn8SpMw_e_bg9kx4ZVPrGHJIu_yOK1FkIlePlN_C7FQ,120
@@ -14,20 +14,20 @@ ngio/common/transforms/_zoom.py,sha256=mbnPnJZsCCms5x1Tq2akvsRDbsDYomiNRGqiF6KY2
 ngio/experimental/__init__.py,sha256=3pmBtHi-i8bKjTsvrOJM56ZyRX3Pv_dceCdt88-8COQ,147
 ngio/experimental/iterators/__init__.py,sha256=on_sUvuRhHBb7-r5u3Ojvu6K9FGjUOrWGUkLQ4aRzbs,556
 ngio/experimental/iterators/_abstract_iterator.py,sha256=p8ZxQuoqPGLZCp79FprhgV-QsN5uuqadffoXnEqSdys,5533
-ngio/experimental/iterators/_feature.py,sha256=6uONbB527SS2NLlpiFtL3AVOazH-QpGhETLEt8pykgU,5987
-ngio/experimental/iterators/_image_processing.py,sha256=4U2FCS5pyDes9VJAGbQn7_e8YMs2TU0ocVr2m1QZhYA,6639
-ngio/experimental/iterators/_rois_utils.py,sha256=LfBKk2XEY-UuomT_9uOg-0b0_GUo6IX5h0OJmrbMs4g,4375
-ngio/experimental/iterators/_segmentation.py,sha256=pCR2eR5LUMV5nouw6vRDjIyIabnvfxp7cE6sukW4GZc,11220
+ngio/experimental/iterators/_feature.py,sha256=5MI0hgcR2lFUQLI4RpVCL2SDJNhmunW33tIUQhPWl_s,5996
+ngio/experimental/iterators/_image_processing.py,sha256=fkD8PDm-3RaKpsRIRzvkeEkvDJ-fzcSWqrMXI3DBM4w,6648
+ngio/experimental/iterators/_rois_utils.py,sha256=yFIlUAsSuh9ArUakJv7kTIiO2yG5r7kuDw-ljmtHj5Y,4359
+ngio/experimental/iterators/_segmentation.py,sha256=NMzHcny2aUCRiSa9dROQ0kMzllYqIEwMh-fUmekw7dY,11229
 ngio/hcs/__init__.py,sha256=G8j9vD-liLeB_UeGtKYIgshWvJnUA6ks9GwjvWBLdHs,357
 ngio/hcs/_plate.py,sha256=qfRwbCKaoz_AWTi8RDFFwOxy5geSknfJrPcqFVno9zI,44288
 ngio/images/__init__.py,sha256=9Whvt7GTiCgT_vXaEEqGnDaY1-UsRk3dhLTv091F_g4,1211
-ngio/images/_abstract_image.py,sha256=AmulSId7WMpKke1ROshxX1hYLHHNQMBy_4F4aPkE-Jw,15601
+ngio/images/_abstract_image.py,sha256=DfKz2xjB4QKMTYn8K9YorQSiPyzcwe9QCDtzzgsCnHE,15615
 ngio/images/_create.py,sha256=X0EalQgrcdh_RVgSxIkv0YNQydKXNRpCXHlgn1oVpI0,9445
 ngio/images/_create_synt_container.py,sha256=XjsQjBEnEGiqrfyKBdp_h4dJmScBMpMg1yUEqObo7Nw,5004
 ngio/images/_image.py,sha256=4PwHsD0KiiJwcyuVX4-iuLCv6V05N6JlCDlEggyLJkw,31742
 ngio/images/_label.py,sha256=rv6-oigkpa5mUTdogdPhfC3JYkEbdjXxY6Y6f1oD-RI,10603
 ngio/images/_masked_image.py,sha256=oFApCcPejfapzilh3ecO2NmI_FReU1FJPc-8XJqsYYU,19619
-ngio/images/_ome_zarr_container.py,sha256=uMQcvfwKj1uL3LG6k7pBQuPfG0KiM94fcf3kP7fu9eg,36705
+ngio/images/_ome_zarr_container.py,sha256=WvvqH73pQkIIyiJTM6Fyzz6wjLs57V3hdEM7YBWzpOo,36712
 ngio/images/_table_ops.py,sha256=jFv_AMqoB4JBpoWsMtZppZVW7dAOC_u-JpfNm8b33kY,15292
 ngio/ome_zarr_meta/__init__.py,sha256=oZ8PEsWM7U0KwzpsnvVfX9k4UfuTz5sZ8B6B9eY5hyY,1193
 ngio/ome_zarr_meta/_meta_handlers.py,sha256=ctknNDT8jxwyvxQf9on5gW31H1tRRsnneO38GT2UXoE,25880
@@ -63,14 +63,14 @@ ngio/tables/v1/__init__.py,sha256=Wr1_9RZFpaN8FYMTnxT9Yjkw4AS7y9FMWailmB_uj5g,61
 ngio/tables/v1/_condition_table.py,sha256=T0Uq5BKkmMoEspt_Rx0U99Ow6S9GAMZDHqvUO5obCAM,1780
 ngio/tables/v1/_feature_table.py,sha256=n9uMHwoBh-_dlOhUXCFbmAjXFVXncNCR3SjE2qzXI68,3821
 ngio/tables/v1/_generic_table.py,sha256=1ktJHeuv7U1g5Z8PFUuTkCjOzcYMQd8xegKHKUedJB8,1240
-ngio/tables/v1/_roi_table.py,sha256=szhtLzHWW-DaDz_OsGK89ur-WpNufCSMvEc66DRzv8g,16867
+ngio/tables/v1/_roi_table.py,sha256=g7UpMmpf3uAfaG59WYRnimUBgiB_T1qUJRwMZpMt9cI,17099
 ngio/utils/__init__.py,sha256=XPYh8ehC7uXNU2cFFXZAw-S3DpWpX1Yq2xGkffZv5vI,1142
 ngio/utils/_datasets.py,sha256=2g-Neg78dNcqyDz39QQw-Ifp9GITHjVHisdqgvvDNDE,5475
 ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_fractal_fsspec_store.py,sha256=RdcCFOgHexRKX9zZvJV5RI-5OPc7VOPS6q_IeRxm24I,1548
 ngio/utils/_logger.py,sha256=N5W0a_xwze4blS1MolidBkTMbjTbg8GPguJZNun3mAE,1392
 ngio/utils/_zarr_utils.py,sha256=aYHhjHWGy5Jx7IkPb4nt9N0-HgyvJnyvK9GGqnccZkE,13606
-ngio-0.4.0a2.dist-info/METADATA,sha256=Wd5zLtu8OLbjEbgV9Lb5FDlBP9dFT9QU4S8h2358jKc,5868
-ngio-0.4.0a2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.4.0a2.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.4.0a2.dist-info/RECORD,,
+ngio-0.4.0a3.dist-info/METADATA,sha256=PrG0TduDw2_iog0OKt2wF_gse3DW0oshBq158P6BS34,5868
+ngio-0.4.0a3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.4.0a3.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.4.0a3.dist-info/RECORD,,