override raw meta data also for series hdf5 format

CHANGELOG

@@ -1,5 +1,5 @@
 0.1.3
- - format single_hdf5: override meta data provided by user
+ - format series and single hdf5: override raw meta data
  - include background data in determination of data set identifiers
  - save memory by hard-linking background image data in QPSeries
 0.1.2

qpformat/file_formats/series_hdf5_qpimage.py

@@ -34,16 +34,23 @@ def get_qpimage(self, idx):
         if self._bgdata:
             # The user has explicitly chosen different background data
             # using `get_qpimage_raw`.
-            return super(SeriesHdf5Qpimage, self).get_qpimage(idx)
+            qpi = super(SeriesHdf5Qpimage, self).get_qpimage(idx)
         else:
             # We can use the background data stored in the qpimage hdf5 file
-            return self._qpseries.get_qpimage(index=idx).copy()
+            qpi = self._qpseries.get_qpimage(index=idx).copy()
+            # Force meta data
+            for key in self.meta_data:
+                qpi[key] = self.meta_data[key]
+        return qpi
 
     def get_qpimage_raw(self, idx):
         """Return QPImage without background correction"""
         qpi = self._qpseries.get_qpimage(index=idx).copy()
         # Remove previously performed background correction
         qpi.set_bg_data(None)
+        # Force meta data
+        for key in self.meta_data:
+            qpi[key] = self.meta_data[key]
         return qpi
 
     @staticmethod

qpformat/file_formats/single_hdf5_qpimage.py

@@ -22,17 +22,21 @@ def get_qpimage(self, idx=0):
         if self._bgdata:
             # The user has explicitly chosen different background data
             # using `get_qpimage_raw`.
-            return super(SingleHdf5Qpimage, self).get_qpimage()
+            qpi = super(SingleHdf5Qpimage, self).get_qpimage()
         else:
             # We can use the background data stored in the qpimage hdf5 file
-            return qpimage.QPImage(h5file=self.path, h5mode="r").copy()
+            qpi = qpimage.QPImage(h5file=self.path, h5mode="r").copy()
+            # Force meta data
+            for key in self.meta_data:
+                qpi[key] = self.meta_data[key]
+        return qpi
 
     def get_qpimage_raw(self, idx=0):
         """Return QPImage without background correction"""
         qpi = qpimage.QPImage(h5file=self.path, h5mode="r").copy()
         # Remove previously performed background correction
         qpi.set_bg_data(None)
-        # Set meta data
+        # Force meta data
         for key in self.meta_data:
             qpi[key] = self.meta_data[key]
         return qpi

tests/test_series_hdf5_qpimage.py

@@ -6,6 +6,30 @@
 import qpformat
 
 
+def test_identifier():
+    path = join(dirname(abspath(__file__)), "data/single_qpimage.h5")
+    tf = tempfile.mktemp(suffix=".h5", prefix="qpformat_test_")
+    qpi1 = qpimage.QPImage(h5file=path, h5mode="r")
+    qpi2 = qpi1.copy()
+    qpi2["identifier"] = "an important string"
+    # generate qpseries hdf5 file
+    with qpimage.QPSeries(qpimage_list=[qpi1, qpi2],
+                          h5file=tf,
+                          h5mode="a"):
+        pass
+
+    ds = qpformat.load_data(tf)
+    assert ds.get_identifier(0) != "an important string"
+    assert ds.get_identifier(1) == "an important string"
+    assert ds.identifier in ds.get_identifier(0)
+
+    # cleanup
+    try:
+        os.remove(tf)
+    except OSError:
+        pass
+
+
 def test_load_data():
     path = join(dirname(abspath(__file__)), "data/single_qpimage.h5")
     tf = tempfile.mktemp(suffix=".h5", prefix="qpformat_test_")
@@ -29,22 +53,33 @@ def test_load_data():
         pass
 
 
-def test_identifier():
+def test_meta_override():
     path = join(dirname(abspath(__file__)), "data/single_qpimage.h5")
     tf = tempfile.mktemp(suffix=".h5", prefix="qpformat_test_")
-    qpi1 = qpimage.QPImage(h5file=path, h5mode="r")
-    qpi2 = qpi1.copy()
-    qpi2["identifier"] = "an important string"
+    qpi = qpimage.QPImage(h5file=path, h5mode="r")
     # generate qpseries hdf5 file
-    with qpimage.QPSeries(qpimage_list=[qpi1, qpi2],
+    with qpimage.QPSeries(qpimage_list=[qpi, qpi],
                           h5file=tf,
-                          h5mode="a"):
+                          h5mode="a",
+                          meta_data={"wavelength": 111e-9,
+                                     "pixel size": .12}):
         pass
 
-    ds = qpformat.load_data(tf)
-    assert ds.get_identifier(0) != "an important string"
-    assert ds.get_identifier(1) == "an important string"
-    assert ds.identifier in ds.get_identifier(0)
+    wl = 333e-9
+    px = .111
+    ds = qpformat.load_data(tf, meta_data={"wavelength": wl,
+                                           "pixel size": px})
+
+    assert ds.meta_data["wavelength"] == wl
+    assert ds.meta_data["pixel size"] == px
+
+    qpi_ds = ds.get_qpimage(0)
+    assert qpi_ds["wavelength"] == wl
+    assert qpi_ds["pixel size"] == px
+
+    qpi_ds = ds.get_qpimage(1)
+    assert qpi_ds["wavelength"] == wl
+    assert qpi_ds["pixel size"] == px
 
     # cleanup
     try:

tests/test_single_hdf5_qpimage.py

@@ -6,6 +6,28 @@
 import qpformat
 
 
+def test_identifier():
+    path = join(dirname(abspath(__file__)), "data/single_qpimage.h5")
+    tf = tempfile.mktemp(suffix=".h5", prefix="qpformat_test_")
+    qpi = qpimage.QPImage(h5file=path, h5mode="r").copy()
+    qpi["identifier"] = "an extremely important string"
+    qpi.copy(tf)
+
+    ds1 = qpformat.load_data(path)
+    ds2 = qpformat.load_data(tf)
+
+    assert ds1.identifier != ds2.identifier
+    assert ds2.identifier == "an extremely important string"
+    assert ds1.identifier == ds1.get_identifier()
+    assert ds2.identifier == ds2.get_identifier()
+
+    # cleanup
+    try:
+        os.remove(tf)
+    except OSError:
+        pass
+
+
 def test_load_data():
     path = join(dirname(abspath(__file__)), "data/single_qpimage.h5")
     ds = qpformat.load_data(path)
@@ -15,20 +37,23 @@ def test_load_data():
     assert ds.get_qpimage() == qpimage.QPImage(h5file=path, h5mode="r")
 
 
-def test_identifier():
+def test_meta_override():
     path = join(dirname(abspath(__file__)), "data/single_qpimage.h5")
     tf = tempfile.mktemp(suffix=".h5", prefix="qpformat_test_")
     qpi = qpimage.QPImage(h5file=path, h5mode="r").copy()
-    qpi["identifier"] = "an extremely important string"
     qpi.copy(tf)
 
-    ds1 = qpformat.load_data(path)
-    ds2 = qpformat.load_data(tf)
+    wl = 333e-9
+    px = .111
+    ds = qpformat.load_data(tf, meta_data={"wavelength": wl,
+                                           "pixel size": px})
 
-    assert ds1.identifier != ds2.identifier
-    assert ds2.identifier == "an extremely important string"
-    assert ds1.identifier == ds1.get_identifier()
-    assert ds2.identifier == ds2.get_identifier()
+    assert ds.meta_data["wavelength"] == wl
+    assert ds.meta_data["pixel size"] == px
+
+    qpi_ds = ds.get_qpimage(0)
+    assert qpi_ds["wavelength"] == wl
+    assert qpi_ds["pixel size"] == px
 
     # cleanup
     try: