Fixes for position metadata

OmeSliCC/OmeSource.py

@@ -92,9 +92,9 @@ def _get_ome_metadata(self):
 
         position = []
         for plane in ensure_list(pixels.get('Plane', [])):
-            position = [(plane.get('PositionX'), plane.get('PositionXUnit')),
-                        (plane.get('PositionY'), plane.get('PositionYUnit')),
-                        (plane.get('PositionZ'), plane.get('PositionZUnit'))]
+            position = [(float(plane.get('PositionX')), plane.get('PositionXUnit')),
+                        (float(plane.get('PositionY')), plane.get('PositionYUnit')),
+                        (float(plane.get('PositionZ')), plane.get('PositionZUnit'))]
             c, z, t = plane.get('TheC'), plane.get('TheZ'), plane.get('TheT')
 
         self.position = position
@@ -211,6 +211,9 @@ def get_pixel_size(self) -> list:
     def get_pixel_size_micrometer(self):
         return get_value_units_micrometer(self.get_pixel_size())
 
+    def get_position_micrometer(self):
+        return get_value_units_micrometer(self.position)
+
     def get_shape(self, dimension_order: str = None, xyzct: tuple = None) -> tuple:
         shape = []
         if dimension_order is None:

OmeSliCC/OmeZarr.py

@@ -48,10 +48,10 @@ def write(self, sources, tile_size=[], compression=[],
             else:
                 root = zarr_root
             if index < len(translations):
-                translation = translations[index]
+                translation_um = translations[index]
             else:
-                translation = []
-            self.write_dataset(root, data, source, npyramid_add, pyramid_downsample, translation)
+                translation_um = source.get_position_micrometer()
+            self.write_dataset(root, data, source, npyramid_add, pyramid_downsample, translation_um)
             if multiple_images:
                 meta = root.attrs['multiscales'][0].copy()
                 for dataset_meta in meta['datasets']:
@@ -62,7 +62,7 @@ def write(self, sources, tile_size=[], compression=[],
         zarr_root.attrs['omero'] = create_channel_metadata(sources[0], ome_version)
 
     def write_dataset(self, zarr_root, data, source,
-                      npyramid_add=0, pyramid_downsample=2, translation=[]):
+                      npyramid_add=0, pyramid_downsample=2, translation_um=[]):
 
         pixel_size_um = source.get_pixel_size_micrometer()
         if len(pixel_size_um) == 0:
@@ -79,7 +79,7 @@ def write_dataset(self, zarr_root, data, source,
         pixel_size_scales = []
         scale = 1
         for i in range(npyramid_add + 1):
-            pixel_size_scales.append(create_transformation_metadata(dimension_order, pixel_size_um, scale, translation))
+            pixel_size_scales.append(create_transformation_metadata(dimension_order, pixel_size_um, scale, translation_um))
             if pyramid_downsample:
                 scale /= pyramid_downsample
 

OmeSliCC/OmeZarrSource.py

@@ -77,25 +77,31 @@ def __init__(self, filename: str,
 
     def _find_metadata(self):
         pixel_size = []
+        position = []
         channels = []
         metadata = self.metadata
         axes = self.dimension_order
 
         units = [axis.get('unit', '') for axis in metadata.get('axes', [])]
 
-        scale1 = [1, 1, 1, 1, 1]
+        scale1 = [1] * len(metadata.get('axes'))
+        position1 = [0] * len(metadata.get('axes'))
         # get pixelsize using largest/first scale
         transform = self.metadata.get('coordinateTransformations', [])
         if transform:
             for transform1 in transform[0]:
                 if transform1['type'] == 'scale':
                     scale1 = transform1['scale']
+                if transform1['type'] == 'translation':
+                    position1 = transform1['translation']
             for axis in 'xyz':
                 if axis in axes:
                     index = axes.index(axis)
                     pixel_size.append((scale1[index], units[index]))
+                    position.append((position1[index], units[index]))
                 else:
                     pixel_size.append((1, ''))
+                    position.append((0, ''))
         nchannels = self.sizes_xyzct[0][3]
         # look for channel metadata
         for data in self.root_metadata.values():
@@ -117,10 +123,10 @@ def _find_metadata(self):
         self.source_pixel_size = pixel_size
         self.channels = channels
         self.source_mag = 0
+        self.position = position
 
     def get_source_dask(self):
-        return [redimension_data(level, self.dimension_order, self.get_dimension_order())
-                for level in self.levels]
+        return self.levels
 
     def _asarray_level(self, level: int, **slicing) -> np.ndarray:
         redim = redimension_data(self.levels[level], self.dimension_order, self.get_dimension_order())

OmeSliCC/Zarr.py

@@ -45,6 +45,7 @@ def create(self, source, shapes=[], chunk_shapes=[], level_scales=[],
         shape0 = [xyzct['xyzct'.index(dimension)] for dimension in dimension_order]
         dtype = source.pixel_types[0]
         pixel_size_um = source.get_pixel_size_micrometer()
+        translation_um = source.get_position_micrometer()
         scale = 1
         datasets = []
         if tile_size and len(tile_size) < 5:
@@ -80,7 +81,7 @@ def create(self, source, shapes=[], chunk_shapes=[], level_scales=[],
             # used for ome metadata:
             datasets.append({
                 'path': str(level),
-                'coordinateTransformations': create_transformation_metadata(dimension_order, pixel_size_um, scale)
+                'coordinateTransformations': create_transformation_metadata(dimension_order, pixel_size_um, scale, translation_um)
             })
             scale /= pyramid_downsample
 

OmeSliCC/conversion.py

@@ -160,7 +160,7 @@ def combine_images(sources: list[OmeSource], params: dict):
     nchannels = len(channels)
 
     if image.shape[1] != nchannels:
-        logging.warning('#Comined image channels does not match #data channels')
+        logging.warning('#Combined image channels does not match #data channels')
 
     new_source.channels = channels
 

OmeSliCC/image_util.py

@@ -320,6 +320,7 @@ def create_compression_codecs(compression: list) -> list:
 
 
 def get_tiff_pages(tiff: TiffFile) -> list:
+    # TODO: review so this works for multi-level ome-tiff, tiff-stack, and z pages tiff, then later check for mmstack
     pages = []
     found = False
     if tiff.series and not tiff.is_mmstack:

OmeSliCC/ome_zarr_util.py

@@ -20,7 +20,7 @@ def create_axes_metadata(dimension_order):
     return axes
 
 
-def create_transformation_metadata(dimension_order, pixel_size_um, scale, translation=[]):
+def create_transformation_metadata(dimension_order, pixel_size_um, scale, translation_um=[]):
     metadata = []
     pixel_size_scale = []
     translation_scale = []
@@ -37,12 +37,12 @@ def create_transformation_metadata(dimension_order, pixel_size_um, scale, transl
             pixel_size_scale1 = 1
         pixel_size_scale.append(pixel_size_scale1)
 
-        if dimension == 'z' and len(translation) > 2:
-            translation1 = translation[2]
-        elif dimension == 'y' and len(translation) > 1:
-            translation1 = translation[1] / scale
-        elif dimension == 'x' and len(translation) > 0:
-            translation1 = translation[0] / scale
+        if dimension == 'z' and len(translation_um) > 2:
+            translation1 = translation_um[2]
+        elif dimension == 'y' and len(translation_um) > 1:
+            translation1 = translation_um[1] * scale
+        elif dimension == 'x' and len(translation_um) > 0:
+            translation1 = translation_um[0] * scale
         else:
             translation1 = 0
         translation_scale.append(translation1)