Add limited support for nexus files

setup.py

@@ -16,7 +16,8 @@ VERSION = '0.0.3'
 
 # What packages are required for this module to be executed?
 REQUIRED = [
-    'attrs', 'numpy', 'asapo_consumer', 'asapo_producer', 'scikit-image'
+    'attrs', 'numpy', 'asapo_consumer', 'asapo_producer', 'scikit-image',
+    'h5py'
 ]
 
 # What packages are optional?

src/AsapoWorker/data_handler.py

 import io
 import numpy as np
+import h5py
 from skimage.io import imread
 
 
@@ -12,11 +13,29 @@ def get_image(data, metadata):
         shape = metadata["meta"]["shape"]
         dtype = metadata["meta"]["dtype"]
         image = np.frombuffer(data, dtype=dtype).reshape(shape)
+    elif typ == "nxs":
+        buf = io.BytesIO(data)
+        h5file = h5py.File(buf)
+        image = get_default_data(h5file)
     else:
         raise ValueError("Unknown extension: " + typ)
     return image
 
 
+def get_default_data(group):
+    default_name = group.attrs.get("default", None)
+    if default_name:
+        return get_default_data(group[default_name])
+    signal_name = group.attrs.get("signal", "data")
+    signal = group[signal_name]
+    if signal.ndim == 1:
+        axis_name = group.attrs.get("axes", "axis")[0]
+        axis = group[axis_name]
+        return np.vstack((axis, signal)).T
+    else:
+        return np.asarray(signal)
+
+
 def get_filename_parts(metadata):
     name = metadata["name"]
     base, sep, index_and_ext = name.rpartition("-")