Removed trivial diffs from chaeo_extension

model_server/base/accessors.py

@@ -34,8 +34,6 @@ class GenericImageDataAccessor(ABC):
     def is_3d(self):
         return True if self.shape_dict['Z'] > 1 else False
 
-    # TODO: implement is_probability
-
     def is_mask(self):
         return is_mask(self._data)
 
@@ -117,6 +115,10 @@ class TifSingleSeriesFileAccessor(GenericImageFileAccessor):
             axs.append('C')
             da = np.expand_dims(da, len(da.shape))
 
+        if 'Z' not in axs:
+            axs.append('Z')
+            da = np.expand_dims(da, len(da.shape))
+
         yxcz = np.moveaxis(
             da,
             [axs.index(k) for k in order],

model_server/base/batch.py

-def get_tif_seq(where, prefix=None, verbose=True):
-    files = [ff for ff in os.listdir(where) if ff.startswith(prefix)]
-    files.sort()
-    paths = [where / fn for fn in files]
-    ndas = [imread(pa.__str__()) for pa in paths]
-    assert all([n.shape == ndas[0].shape and n.dtype == ndas[0].dtype for n in ndas])
-    if verbose:
-        print(f'Successfully read {len(ndas)} x {ndas[0].shape} px images of type {ndas[0].dtype} from:\n{where}')
-    return ndas
-
-def write_tif_zstack(data, desc, dtype='uint16', subdir='output'):
-    where = root / subdir
-    filename = desc + '.tif'
-    if not os.path.exists(where):
-        os.makedirs(where)
-    abspath = where / filename
-    imwrite(
-        abspath,
-        np.array(data).astype(dtype),
-        imagej=True
-    )
-    print(f'Successfully wrote {len(data)} x {data[0].shape} px images of type {dtype} to:\n{abspath}')
\ No newline at end of file