feat: support subjoined QPSeries file format

CHANGELOG

@@ -1,3 +1,5 @@
+0.7.0
+ - feat: support subjoined QPSeries file format
 0.6.4
  - fix: ignore None or nan values in given meta data
 0.6.3

qpformat/file_formats/__init__.py

@@ -5,7 +5,7 @@
 from .dataset import SeriesData, hash_obj
 from .dataset import SingleData  # noqa:F401 (user convenience)
 from .series_hdf5_hyperspy import SeriesHdf5HyperSpy
-from .series_hdf5_qpimage import SeriesHdf5Qpimage
+from .series_hdf5_qpimage import SeriesHdf5Qpimage, SeriesHdf5QpimageSubjoined
 from .series_zip_tif_holo import SeriesZipTifHolo
 from .series_zip_tif_phasics import SeriesZipTifPhasics
 from .single_hdf5_qpimage import SingleHdf5Qpimage
@@ -199,6 +199,7 @@ def verify(path):
            SingleNpyNumpy,
            SeriesHdf5HyperSpy,
            SeriesHdf5Qpimage,
+           SeriesHdf5QpimageSubjoined,
            SeriesZipTifPhasics,
            SeriesZipTifHolo,  # after phasics, b/c phasics has extra keywords
            ]

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
+        self._init_meta()
+
+    def __len__(self):
+        with self._qpseries() as qps:
+            return len(qps)
+
+    def _init_meta(self):
         # update meta data
         with h5py.File(self.path, mode="r") as h5:
             attrs = dict(h5["qpi_0"].attrs)
@@ -19,10 +26,6 @@ def __init__(self, *args, **kwargs):
                     and key in attrs):
                 self.meta_data[key] = attrs[key]
 
-    def __len__(self):
-        with self._qpseries() as qps:
-            return len(qps)
-
     def _qpseries(self):
         return qpimage.QPSeries(h5file=self.path, h5mode="r")
 
@@ -73,3 +76,39 @@ def verify(path):
                     "bg_data" in qpi0["amplitude"]):
                 valid = True
         return valid
+
+
+class SeriesHdf5QpimageSubjoined(SeriesHdf5Qpimage):
+    """Subjoined qpimage series (HDF5 format), may contain other data"""
+
+    def _init_meta(self):
+        # update meta data
+        with h5py.File(self.path, mode="r") as h5:
+            attrs = dict(h5["qpseries/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 _qpseries(self):
+        h5 = h5py.File(self.path, mode="r")
+        return qpimage.QPSeries(h5file=h5["qpseries"])
+
+    @staticmethod
+    def verify(path):
+        """Verify that `path` has the qpimage series file format"""
+        valid = False
+        try:
+            h5 = h5py.File(path, mode="r")
+            qps = h5["qpseries"]
+            qpi0 = qps["qpi_0"]
+        except (OSError, KeyError):
+            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

@@ -2,6 +2,7 @@
 import pathlib
 import tempfile
 
+import h5py
 import numpy as np
 
 import qpimage
@@ -152,6 +153,38 @@ def test_returned_identifier():
         pass
 
 
+def test_subjoined_load_data():
+    path = datapath / "single_qpimage.h5"
+    tf = tempfile.mktemp(suffix=".h5", prefix="qpformat_test_subjoined")
+    qpi1 = qpimage.QPImage(h5file=path, h5mode="r").copy()
+    qpi2 = qpi1.copy()
+    qpi1["identifier"] = "test100"
+    qpi2["identifier"] = "test200"
+    # generate subjoined qpseries hdf5 file
+    with h5py.File(tf, mode="w") as h5:
+        qps = h5.require_group("qpseries")
+        qpimage.QPSeries(qpimage_list=[qpi1, qpi2],
+                         h5file=qps)
+
+    ds = qpformat.load_data(tf)
+    assert len(ds) == 2
+    assert ds.path == pathlib.Path(tf)
+    assert np.isnan(ds.get_time(1))
+    assert "SeriesHdf5QpimageSubjoined" in ds.__repr__()
+    qpd = ds.get_qpimage(1)
+    assert qpd["identifier"] != qpi1["identifier"]
+    assert qpd == qpi1
+    assert qpd.shape == qpi1.shape
+    assert np.allclose(qpd.amp, qpi1.amp)
+    assert np.allclose(qpd.pha, qpi1.pha)
+
+    # cleanup
+    try:
+        os.remove(tf)
+    except OSError:
+        pass
+
+
 if __name__ == "__main__":
     # Run all tests
     loc = locals()