Fix 419

dascore/data_registry.txt

@@ -25,3 +25,4 @@ silixa_h5_1.hdf5 d3f1b92b17ae2d00f900426e80d48964fb5a33b9480ef9805721ac756acd4a2
 deformation_rate_event_1.hdf5 be8574ae523de9b17d2a0f9e847f30301e1607e2076366e005cdb3a46b79f172 https://github.com/dasdae/test_data/raw/master/das/deformation_rate_event_1.hdf5
 neubrex_dss_forge.h5 49e501e16d880b22c5d9d8997223f0c1aceb942386efb09aae938b9d97eb51ed https://github.com/dasdae/test_data/raw/master/dss/neubrex_dss_forge.h5
 neubrex_dts_forge.h5 940f7bea6dd4c8a1340b4936b8eb7f9edc577cbcaf77c1f5ac295890f88c9ba5 https://github.com/dasdae/test_data/raw/master/dts/neubrex_dts_forge.h5
+decimated_optodas.hdf5 48ce9c2ab4916d5536faeef0bd789f326ec4afc232729d32014d4d835a9fb74e https://github.com/dasdae/test_data/raw/master/das/decimated_optodas.hdf5

dascore/io/optodas/utils.py

@@ -27,30 +27,30 @@ def _get_opto_das_version_str(hdf_fi) -> str:
     return version_str
 
 
-def _get_coord_manager(header):
+def _get_coord_manager(fi):
     """Get the distance ranges and spacing."""
+    header = fi["header"]
     dims = tuple(unbyte(x) for x in header["dimensionNames"])
     units = tuple(unbyte(x) for x in header["dimensionUnits"])
-
     coords = {}
     for index, (dim, unit) in enumerate(zip(dims, units)):
         crange = header["dimensionRanges"][f"dimension{index}"]
         step = unpack_scalar_h5_dataset(crange["unitScale"])
 
-        # special case for time.
+        # Special case for time.
         if dim == "time":
             step = dc.to_timedelta64(step)
             t1 = dc.to_datetime64(unpack_scalar_h5_dataset(header["time"]))
             start = t1 + unpack_scalar_h5_dataset(crange["min"]) * step
             stop = t1 + (unpack_scalar_h5_dataset(crange["max"]) + 1) * step
-        else:
-            # The min/max values appear to be int ranges so we need to
-            # multiply by step.
-            start = unpack_scalar_h5_dataset(crange["min"]) * step
-            stop = (unpack_scalar_h5_dataset(crange["max"]) + 1) * step
-
-        coords[dim] = get_coord(min=start, max=stop, step=step, units=unit)
-    return dascore.core.get_coord_manager(coords=coords, dims=dims)
+            coord = get_coord(min=start, max=stop, step=step, units=unit)
+        else:  # and distance
+            # The channels are ints so we multiply by step to get distance.
+            distance = fi["/header/channels"][:] * step
+            coord = get_coord(values=distance)
+        coords[dim] = coord
+    out = dascore.core.get_coord_manager(coords=coords, dims=dims)
+    return out
 
 
 def _get_attr_dict(header):
@@ -72,9 +72,8 @@ def _get_attr_dict(header):
 
 def _get_opto_das_attrs(fi) -> dict:
     """Scan a OptoDAS file, return metadata."""
-    header = fi["header"]
-    cm = _get_coord_manager(header)
-    attrs = _get_attr_dict(header)
+    cm = _get_coord_manager(fi)
+    attrs = _get_attr_dict(fi["header"])
     attrs["coords"] = cm
     return attrs
 

tests/test_io/test_optodas/test_optodas.py

@@ -0,0 +1,24 @@
+"""
+Tests for optoDAS files.
+"""
+
+import dascore as dc
+from dascore.io.optodas import OptoDASV8
+from dascore.utils.downloader import fetch
+
+
+class TestOptoDASIssues:
+    """Test case related to issues in OptoDAS parser."""
+
+    def test_read_decimated_patch(self):
+        """Tests for reading spatially decimated patch (#419)"""
+        path = fetch("decimated_optodas.hdf5")
+        fiber_io = OptoDASV8()
+
+        fmt_str, version_str = fiber_io.get_format(path)
+        assert (fmt_str, version_str) == (fiber_io.name, fiber_io.version)
+
+        spool = fiber_io.read(path)
+        patch = spool[0]
+        assert isinstance(patch, dc.Patch)
+        assert patch.data.shape