add support for qpimage.QPSeries hdf5 file format

qpformat/file_formats/__init__.py

@@ -2,7 +2,7 @@
 import os.path as op
 
 from .dataset import DataSet
-# from .series_hdf5_qpimage import SeriesHdf5Qpimage
+from .series_hdf5_qpimage import SeriesHdf5Qpimage
 from .series_zip_tif_phasics import SeriesZipTifPhasics
 from .single_hdf5_qpimage import SingleHdf5Qpimage
 from .single_tif_phasics import SingleTifPhasics
@@ -89,7 +89,7 @@ class UnknownFileFormatError(BaseException):
 # the order is important for
 formats = [SeriesFolder,
            SeriesZipTifPhasics,
-           # SeriesHdf5Qpimage,
+           SeriesHdf5Qpimage,
            SingleHdf5Qpimage,
            SingleTifPhasics,
            ]

qpformat/file_formats/series_hdf5_qpimage.py

@@ -1,5 +1,61 @@
-from dataset import DataSet
+import h5py
+import qpimage
+
+from .dataset import DataSet
 
 
 class SeriesHdf5Qpimage(DataSet):
-    pass
+    def __init__(self, *args, **kwargs):
+        super(SeriesHdf5Qpimage, self).__init__(*args, **kwargs)
+        self._qpseries = qpimage.QPSeries(h5file=self.path,
+                                          h5mode="r")
+        self._dataset = None
+
+    def __len__(self):
+        return len(self._qpseries)
+
+    def get_qpimage(self, idx=0):
+        """Return background-corrected QPImage of data at index `idx`"""
+        if self._bgdata:
+            # The user has explicitly chosen different background data
+            # using `get_qpimage_raw`.
+            return 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()
+
+    def get_qpimage_raw(self, idx=0):
+        """Return QPImage without background correction"""
+        qpi = self._qpseries.get_qpimage(index=idx).copy()
+        # Remove previously performed background correction
+        qpi.set_bg_data(None)
+        return qpi
+
+    def get_time(self, idx=0):
+        """Return the time of the QPImage data"""
+        qpi = self._qpseries.get_qpimage(index=idx)
+        if "time" in qpi.meta:
+            return qpi.meta["time"]
+        else:
+            return 0
+
+    @staticmethod
+    def verify(path):
+        """Verify that `path` has the qpimage file format
+
+        Returns `True` if the file format matches.
+        """
+        valid = False
+        try:
+            h5 = h5py.File(path, mode="r")
+            qpi0 = h5["qpi_0"]
+        except:
+            pass
+        else:
+            if ("qpimage version" in qpi0.attrs and
+                "phase" in qpi0 and
+                "amplitude" in qpi0 and
+                "bg_data" in qpi0["phase"] and
+                    "bg_data" in qpi0["amplitude"]):
+                valid = True
+        return valid

tests/test_series_hdf5_qpimage.py

@@ -0,0 +1,41 @@
+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
+
+
+def test_load_data():
+    path = join(dirname(abspath(__file__)), "data/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"):
+        pass
+
+    ds = qpformat.load_data(tf)
+    assert len(ds) == 2
+    assert ds.path == tf
+    assert ds.get_time(1) == 0
+    assert "SeriesHdf5Qpimage" in ds.__repr__()
+    assert ds.get_qpimage(1) == qpi
+    # cleanup
+    try:
+        os.remove(tf)
+    except:
+        pass
+
+
+if __name__ == "__main__":
+    # Run all tests
+    loc = locals()
+    for key in list(loc.keys()):
+        if key.startswith("test_") and hasattr(loc[key], "__call__"):
+            loc[key]()