improve coverage, add hdf5 identifiers

CHANGELOG

@@ -1,6 +1,8 @@
 0.1.2
  - implement SeriesData.saveh5 (export as qpimage.QPSeries) (#2)
  - add unique part of file name to SeriesFolder image identifiers (#2)
+ - change API for SingleData ("idx=0" for user convenience)
+ - extract identifiers from hdf5 files
 0.1.1
  - support pathlib on high level
  - add SeriesData.identifier

qpformat/file_formats/series_hdf5_qpimage.py

@@ -14,6 +14,21 @@ def __init__(self, *args, **kwargs):
     def __len__(self):
         return len(self._qpseries)
 
+    @property
+    def identifier(self):
+        identifier = self._qpseries.identifier
+        if identifier is None:
+            identifier = super(SeriesHdf5Qpimage, self).identifier
+        return identifier
+
+    def get_identifier(self, idx):
+        """Return an identifier for the data at index `idx`"""
+        if "identifier" in self._qpseries[idx]:
+            identifier = self._qpseries[idx]["identifier"]
+        else:
+            identifier = super(SeriesHdf5Qpimage, self).get_identifier(idx)
+        return identifier
+
     def get_qpimage(self, idx):
         """Return background-corrected QPImage of data at index `idx`"""
         if self._bgdata:

qpformat/file_formats/single_hdf5_qpimage.py

@@ -5,6 +5,18 @@
 
 
 class SingleHdf5Qpimage(SingleData):
+    @property
+    def identifier(self):
+        with qpimage.QPImage(h5file=self.path, h5mode="r") as qpi:
+            if "identifier" in qpi:
+                identifier = qpi["identifier"]
+            else:
+                identifier = super(SingleHdf5Qpimage, self).identifier
+        return identifier
+
+    def get_identifier(self, idx=0):
+        return self.identifier
+
     def get_qpimage(self, idx=0):
         """Return background-corrected QPImage"""
         if self._bgdata:

tests/test_series_hdf5_qpimage.py

@@ -1,13 +1,9 @@
 import os
 from os.path import abspath, dirname, join
-import sys
 import tempfile
 
 import qpimage
-
-# Add parent directory to beginning of path variable
-sys.path.insert(0, dirname(dirname(abspath(__file__))))
-import qpformat  # noqa: E402
+import qpformat
 
 
 def test_load_data():
@@ -33,6 +29,30 @@ def test_load_data():
         pass
 
 
+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
+
+
 if __name__ == "__main__":
     # Run all tests
     loc = locals()

tests/test_single_hdf5_qpimage.py

@@ -1,9 +1,9 @@
+import os
 from os.path import abspath, dirname, join
-import sys
+import tempfile
 
-# Add parent directory to beginning of path variable
-sys.path.insert(0, dirname(dirname(abspath(__file__))))
-import qpformat  # noqa: E402
+import qpimage
+import qpformat
 
 
 def test_load_data():
@@ -12,6 +12,29 @@ def test_load_data():
     assert ds.path == path
     assert ds.get_time() == 0
     assert "SingleHdf5Qpimage" in ds.__repr__()
+    assert ds.get_qpimage() == qpimage.QPImage(h5file=path, h5mode="r")
+
+
+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
 
 
 if __name__ == "__main__":