Add possibility to change the boundingbox of a layer (#225)

* add possibility to change the boundingbox of a layer

* make offset and size optional parameter when changing the boundingbox

* split changing boundingbox size and offset into different methods

Author: rschwanhold

tests/test_dataset.py

@@ -1146,3 +1146,52 @@ def test_tiled_tiff_dataset_get_or_create():
         raise Exception(expected_error_msg)
     except AssertionError:
         pass
+
+
+def test_changing_layer_bounding_box():
+    delete_dir("./testoutput/test_changing_layer_bounding_box/")
+    copytree(
+        "./testdata/simple_tiff_dataset/",
+        "./testoutput/test_changing_layer_bounding_box/",
+    )
+
+    ds = TiffDataset("./testoutput/test_changing_layer_bounding_box/")
+    layer = ds.get_layer("color")
+    mag = layer.get_mag("1")
+
+    bbox_size = ds.properties.data_layers["color"].get_bounding_box_size()
+    assert bbox_size == (265, 265, 10)
+    original_data = mag.read(bbox_size)
+    assert original_data.shape == (1, 265, 265, 10)
+
+    layer.set_bounding_box_size((100, 100, 10))  # decrease boundingbox
+
+    bbox_size = ds.properties.data_layers["color"].get_bounding_box_size()
+    assert bbox_size == (100, 100, 10)
+    less_data = mag.read(bbox_size)
+    assert less_data.shape == (1, 100, 100, 10)
+    assert np.array_equal(original_data[:, :100, :100, :10], less_data)
+
+    layer.set_bounding_box_size((300, 300, 10))  # increase the boundingbox
+
+    bbox_size = ds.properties.data_layers["color"].get_bounding_box_size()
+    assert bbox_size == (300, 300, 10)
+    more_data = mag.read(bbox_size)
+    assert more_data.shape == (1, 300, 300, 10)
+    assert np.array_equal(more_data[:, :265, :265, :10], original_data)
+
+    layer.set_bounding_box_size((300, 300, 10))  # increase the boundingbox
+
+    assert ds.properties.data_layers["color"].get_bounding_box_offset() == (0, 0, 0)
+
+    layer.set_bounding_box(
+        offset=(10, 10, 0), size=(255, 255, 10)
+    )  # change offset and size
+
+    new_bbox_offset = ds.properties.data_layers["color"].get_bounding_box_offset()
+    new_bbox_size = ds.properties.data_layers["color"].get_bounding_box_size()
+    assert new_bbox_offset == (10, 10, 0)
+    assert new_bbox_size == (255, 255, 10)
+    new_data = mag.read(new_bbox_size)
+    assert new_data.shape == (1, 255, 255, 10)
+    assert np.array_equal(original_data[:, 10:, 10:, :], new_data)

wkcuber/api/Layer.py

@@ -1,6 +1,10 @@
 from shutil import rmtree
 from os.path import join
 from os import makedirs
+from typing import Tuple
+
+import numpy as np
+
 from wkw import wkw
 
 from wkcuber.api.MagDataset import (
@@ -61,6 +65,28 @@ def _assert_mag_does_not_exist_yet(self, mag):
                 )
             )
 
+    def set_bounding_box(
+        self, offset: Tuple[int, int, int], size: Tuple[int, int, int]
+    ):
+        self.set_bounding_box_offset(offset)
+        self.set_bounding_box_size(size)
+
+    def set_bounding_box_offset(self, offset: Tuple[int, int, int]):
+        size = self.dataset.properties.data_layers["color"].get_bounding_box_size()
+        self.dataset.properties._set_bounding_box_of_layer(
+            self.name, tuple(offset), tuple(size)
+        )
+        for _, mag in self.mags.items():
+            mag.view.global_offset = offset
+
+    def set_bounding_box_size(self, size: Tuple[int, int, int]):
+        offset = self.dataset.properties.data_layers["color"].get_bounding_box_offset()
+        self.dataset.properties._set_bounding_box_of_layer(
+            self.name, tuple(offset), tuple(size)
+        )
+        for _, mag in self.mags.items():
+            mag.view.size = size
+
 
 class WKLayer(Layer):
     def add_mag(