Fix ome ngff schmea location and bump version (#142)

* Fix ome ngff schmea location and bump version

* Fix tests

* More test fixes

Author: constantinpape

mobie/__version__.py

@@ -1,2 +1,2 @@
-__version__ = "0.5.3"
+__version__ = "0.5.4"
 SPEC_VERSION = "0.3.0"

mobie/import_data/traces.py

@@ -118,7 +118,7 @@ def traces_to_volume(traces, out_path, key, shape, resolution, chunks,
                      radius, n_threads, crop_overhanging=True):
     # write temporary h5 dataset
     # and write coordinates (with some radius) to it
-    with open_file(out_path) as f:
+    with open_file(out_path, mode="a") as f:
         ds = f.require_dataset(key, shape=shape, dtype='int16', compression='gzip',
                                chunks=chunks)
         ds.n_threads = n_threads

mobie/validation/utils.py

@@ -13,7 +13,7 @@
     "source": "https://raw.githubusercontent.com/mobie/mobie.github.io/master/schema/source.schema.json",
     "view": "https://raw.githubusercontent.com/mobie/mobie.github.io/master/schema/view.schema.json",
     "views": "https://raw.githubusercontent.com/mobie/mobie.github.io/master/schema/views.schema.json",
-    "NGFF": "https://raw.githubusercontent.com/ome/ngff/main/0.4/schemas/image.schema"
+    "NGFF": "https://raw.githubusercontent.com/ome/ngff/7ac3430c74a66e5bcf53e41c429143172d68c0a4/schemas/image.schema"
 }
 
 

mobie/xml_utils.py

@@ -123,7 +123,7 @@ def update_xml_transformation_parameter(xml_path, parameter):
     else:
         raise ValueError(f"Invalid affine transformation {parameter}")
     resolution = get_resolution(xml_path, setup_id=0)
-    if np.product(resolution) != 1:
+    if np.prod(resolution) != 1:
         warnings.warn(
             f"The xml file at {xml_path} has the resolution {resolution}."
             "The corresponding transformation will be over-written,"

test/import_data/test_image.py

@@ -92,7 +92,7 @@ def create_h5_input_data(self, shape=3*(64,)):
         data = np.random.rand(*shape)
         test_path = os.path.join(self.test_folder, "data-h5.h5")
         key = "data"
-        with open_file(test_path) as f:
+        with open_file(test_path, mode="a") as f:
             f.create_dataset(key, data=data)
         return test_path, key, data
 
@@ -108,11 +108,11 @@ def test_import_tif(self):
         im_folder = os.path.join(self.test_folder, "im-stack")
         os.makedirs(im_folder, exist_ok=True)
 
-        resolution=(0.25, 1, 1)
+        resolution = (0.25, 1, 1)
 
         for z in range(shape[0]):
             path = os.path.join(im_folder, "z_%03i.tif" % z)
-            imageio.imsave(path, data[z])
+            imageio.imwrite(path, data[z])
 
         scales = [[1, 2, 2], [1, 2, 2], [2, 2, 2]]
         import_image_data(im_folder, "*.tif", self.out_path,
@@ -126,7 +126,7 @@ def test_import_hdf5(self):
         from mobie.import_data import import_image_data
         test_path, key, data = self.create_h5_input_data()
         scales = [[2, 2, 2], [2, 2, 2], [2, 2, 2]]
-        resolution=(1, 1, 1)
+        resolution = (1, 1, 1)
         import_image_data(test_path, key, self.out_path,
                           resolution=resolution, chunks=(32, 32, 32),
                           scale_factors=scales, tmp_folder=self.tmp_folder,

test/import_data/test_segmentation.py

@@ -46,7 +46,7 @@ def test_import_segmentation(self):
 
         test_path = os.path.join(self.test_folder, 'data.h5')
         key = 'data'
-        with open_file(test_path) as f:
+        with open_file(test_path, mode="a") as f:
             f.create_dataset(key, data=data)
 
         scales = [[1, 2, 2], [2, 2, 2], [2, 2, 2]]

test/test_image_data.py

@@ -46,7 +46,7 @@ def make_tif_data(self, im_folder, shape):
         os.makedirs(im_folder, exist_ok=True)
         for z in range(shape[0]):
             path = os.path.join(im_folder, "z_%03i.tif" % z)
-            imageio.imsave(path, np.random.rand(*shape[1:]))
+            imageio.imwrite(path, np.random.rand(*shape[1:]))
 
     def test_init_from_tif(self):
         shape = (32, 128, 128)