feat: extract meta data from QPSeries/QPImage data files

CHANGELOG

@@ -1,3 +1,5 @@
+0.4.0
+ - feat: extract meta data from QPSeries/QPImage data files
 0.3.5
  - fix: single_tif_phaiscs (SID4Bio) contains two phase images, the second
    of which is recorded at a different time point than the intensity

qpformat/file_formats/series_hdf5_qpimage.py

@@ -11,6 +11,13 @@ class SeriesHdf5Qpimage(SeriesData):
     def __init__(self, *args, **kwargs):
         super(SeriesHdf5Qpimage, self).__init__(*args, **kwargs)
         self._dataset = None
+        # update meta data
+        with h5py.File(self.path, mode="r") as h5:
+            attrs = dict(h5["qpi_0"].attrs)
+        for key in qpimage.meta.DATA_KEYS:
+            if (key not in self.meta_data
+                    and key in attrs):
+                self.meta_data[key] = attrs[key]
 
     def __len__(self):
         with self._qpseries() as qps:

qpformat/file_formats/single_hdf5_qpimage.py

@@ -12,6 +12,16 @@ class SingleHdf5Qpimage(SingleData):
     """
     storage_type = "phase,amplitude"
 
+    def __init__(self, *args, **kwargs):
+        super(SingleHdf5Qpimage, self).__init__(*args, **kwargs)
+        # update meta data
+        with h5py.File(self.path, mode="r") as h5:
+            attrs = dict(h5.attrs)
+        for key in qpimage.meta.DATA_KEYS:
+            if (key not in self.meta_data
+                    and key in attrs):
+                self.meta_data[key] = attrs[key]
+
     def get_qpimage(self, idx=0):
         """Return background-corrected QPImage"""
         if self._bgdata:

tests/test_series_hdf5_qpimage.py

@@ -67,6 +67,30 @@ def test_load_data():
         pass
 
 
+def test_meta_extraction():
+    path = datapath / "single_qpimage.h5"
+    tf = tempfile.mktemp(suffix=".h5", prefix="qpformat_test_")
+    qpi = qpimage.QPImage(h5file=path, h5mode="r")
+    # generate qpseries hdf5 file
+    with qpimage.QPSeries(qpimage_list=[qpi, qpi],
+                          h5file=tf,
+                          h5mode="a",
+                          meta_data={"wavelength": 111e-9,
+                                     "pixel size": .12}):
+        pass
+
+    ds = qpformat.load_data(tf)
+
+    assert ds.meta_data["wavelength"] == 111e-9
+    assert ds.meta_data["pixel size"] == .12
+
+    # cleanup
+    try:
+        os.remove(tf)
+    except OSError:
+        pass
+
+
 def test_meta_override():
     path = datapath / "single_qpimage.h5"
     tf = tempfile.mktemp(suffix=".h5", prefix="qpformat_test_")

tests/test_single_hdf5_qpimage.py

@@ -51,6 +51,28 @@ def test_load_data():
     assert np.allclose(qpd.pha, qpi.pha)
 
 
+def test_meta_extraction():
+    path = datapath / "single_qpimage.h5"
+    tf = tempfile.mktemp(suffix=".h5", prefix="qpformat_test_")
+    qpi = qpimage.QPImage(h5file=path, h5mode="r").copy()
+    qpi["wavelength"] = 345e-9
+    qpi["pixel size"] = .1e-6
+    qpi["medium index"] = 1.336
+    qpi.copy(tf)
+
+    ds = qpformat.load_data(tf)
+
+    assert ds.meta_data["wavelength"] == 345e-9
+    assert ds.meta_data["pixel size"] == .1e-6
+    assert ds.meta_data["medium index"] == 1.336
+
+    # cleanup
+    try:
+        os.remove(tf)
+    except OSError:
+        pass
+
+
 def test_meta_override():
     path = datapath / "single_qpimage.h5"
     tf = tempfile.mktemp(suffix=".h5", prefix="qpformat_test_")