setup: migrate from qpimage 0.7.4 to 0.7.6

CHANGELOG

@@ -1,3 +1,5 @@
+0.11.1
+ - setup: migrate from qpimage 0.7.4 to 0.7.6
 0.11.0
  - feat: implement FDTD/Meep reader for data from ODTbrain paper
  - fix: remove call to deprecated Element.getchildren

qpformat/file_formats/series_hdf5_generic.py

@@ -33,8 +33,6 @@ def _get_data_indices(self):
             indices = sorted(h5["sinogram"].keys(), key=lambda x: int(x))
 
         if not indices:
-            # if this error is raised, the signal_type is probably not
-            # set to "hologram".
             raise NoSinogramDataFoundError(
                 f"No sinogram data found in '{self.path}'!")
         return indices

qpformat/file_formats/series_hdf5_hyperspy.py

@@ -21,13 +21,13 @@ class SeriesHdf5HyperSpy(SeriesData):
     HyperSpy has its :ref:`own implementation
     <hyperspy:electron-holography-label>` to read this file format.
     """
-    storage_type = "hologram"
+    storage_type = "raw-oah"
 
     def __len__(self):
         return len(self._get_experiments())
 
     def _check_experiment(self, name):
-        """Check the signal type of the experiment
+        """Check the signal type "hologram" of the experiment
 
         Returns
         -------
@@ -89,7 +89,7 @@ def get_qpimage_raw(self, idx=0):
         meta_data.update(self.meta_data)
 
         qpi = qpimage.QPImage(data=data,
-                              which_data="hologram",
+                              which_data="raw-oah",
                               meta_data=meta_data,
                               holo_kw=self.holo_kw,
                               h5dtype=self.as_type)

qpformat/file_formats/series_zip_tif_holo.py

@@ -15,7 +15,7 @@ class SeriesZipTifHolo(SeriesData):
     The data are stored as multiple TIFF files
     (:class:`qpformat.file_formats.SingleTifHolo`) in a zip file.
     """
-    storage_type = "hologram"
+    storage_type = "raw-oah"
 
     def __init__(self, *args, **kwargs):
         super(SeriesZipTifHolo, self).__init__(*args, **kwargs)

qpformat/file_formats/single_tif_holo.py

@@ -11,7 +11,7 @@
 
 class SingleTifHolo(SingleData):
     """Off-axis hologram image (TIFF format)"""
-    storage_type = "hologram"
+    storage_type = "raw-oah"
 
     @staticmethod
     def _get_tif(path):
@@ -44,7 +44,7 @@ def get_qpimage_raw(self, idx=0):
             holo = tf.pages[0].asarray()
         meta_data = copy.copy(self.meta_data)
         qpi = qpimage.QPImage(data=holo,
-                              which_data="hologram",
+                              which_data="raw-oah",
                               meta_data=meta_data,
                               holo_kw=self.holo_kw,
                               h5dtype=self.as_type)

setup.py

@@ -25,7 +25,7 @@
     long_description=open('README.rst').read() if exists('README.rst') else '',
     install_requires=["h5py>=2.7.0",
                       "numpy>=1.12.0",
-                      "qpimage>=0.7.4",
+                      "qpimage>=0.7.6",
                       "tifffile>=2020.5.25",
                       ],
     python_requires='>=3.6, <4',

tests/test_series_zip_tif_holo.py

@@ -31,7 +31,7 @@ def test_basic():
     path = setup_test_zip(num)
     ds = qpformat.load_data(path)
     # basic tests
-    assert ds.storage_type == "hologram"
+    assert ds.storage_type == "raw-oah"
     assert len(ds) == num
     assert ds.is_series
     assert ds.path.samefile(path)

tests/test_single_tif_holo.py

@@ -10,7 +10,7 @@ def test_basic():
     path = datapath / "single_holo.tif"
     ds = qpformat.load_data(path)
     # basic tests
-    assert ds.storage_type == "hologram"
+    assert ds.storage_type == "raw-oah"
     assert not ds.is_series
     assert ds.path == path.resolve()
     assert "SingleTifHolo" in ds.__repr__()