h5py supports pathlib.Path

qpformat/core.py

@@ -8,10 +8,11 @@
 def guess_format(path):
     """Determine the file format of a folder or a file"""
     for fmt in formats:
-        if fmt.verify(str(path)):
+        if fmt.verify(path):
             return fmt.__name__
     else:
-        raise UnknownFileFormatError(str(path))
+        msg = "Undefined file format: '{}'".format(path)
+        raise UnknownFileFormatError(msg)
 
 
 def load_data(path, fmt=None, bg_data=None, bg_fmt=None,
@@ -56,7 +57,7 @@ def load_data(path, fmt=None, bg_data=None, bg_fmt=None,
     if fmt is None:
         fmt = guess_format(path)
 
-    dataobj = formats_dict[fmt](path=str(path),
+    dataobj = formats_dict[fmt](path=path,
                                 meta_data=meta_data,
                                 holo_kw=holo_kw,
                                 as_type=as_type)
@@ -70,7 +71,7 @@ def load_data(path, fmt=None, bg_data=None, bg_fmt=None,
             bg_path = pathlib.Path(bg_data).resolve()
             if bg_fmt is None:
                 bg_fmt = guess_format(bg_path)
-                bgobj = formats_dict[bg_fmt](path=str(bg_path),
+                bgobj = formats_dict[bg_fmt](path=bg_path,
                                              meta_data=meta_data,
                                              holo_kw=holo_kw,
                                              as_type=as_type)

qpformat/file_formats/series_hdf5_hyperspy.py

@@ -95,7 +95,7 @@ def verify(path):
         """
         valid = False
         try:
-            h5 = h5py.File(str(path), mode="r")
+            h5 = h5py.File(path, mode="r")
         except (OSError,):
             pass
         else:

qpformat/file_formats/series_hdf5_qpimage.py

@@ -69,7 +69,7 @@ def verify(path):
         """
         valid = False
         try:
-            h5 = h5py.File(str(path), mode="r")
+            h5 = h5py.File(path, mode="r")
             qpi0 = h5["qpi_0"]
         except (OSError, KeyError):
             pass

qpformat/file_formats/single_hdf5_qpimage.py

@@ -57,7 +57,7 @@ def verify(path):
         """
         valid = False
         try:
-            h5 = h5py.File(str(path), mode="r")
+            h5 = h5py.File(path, mode="r")
         except (OSError,):
             pass
         else:

qpformat/file_formats/single_tif_holo.py

@@ -1,5 +1,5 @@
 import copy
-import pathlib
+from os import fspath
 
 import qpimage
 from skimage.external import tifffile
@@ -13,12 +13,12 @@ class SingleTifHolo(SingleData):
 
     @staticmethod
     def _get_tif(path):
-        if isinstance(path, pathlib.Path):
-            path = str(path)
-        elif not isinstance(path, str):
+        if hasattr(path, "seek"):  # opened file
             # Seek open file zero to avoid error in tifffile:
             # "ValueError: invalid TIFF file"
             path.seek(0)
+        else:  # path
+            path = fspath(path)
         return tifffile.TiffFile(path)
 
     def get_qpimage_raw(self, idx=0):

qpformat/file_formats/single_tif_phasics.py

@@ -1,6 +1,6 @@
 import calendar
 import copy
-import pathlib
+from os import fspath
 import time
 import xml.etree.ElementTree as ET
 
@@ -59,7 +59,7 @@ def __init__(self, path, meta_data={}, *args, **kwargs):
     @staticmethod
     def _get_meta_data(path, section, name):
         with SingleTifPhasics._get_tif(path) as tf:
-            meta = str(tf.pages[0].tags["61238"].value)
+            meta = tf.pages[0].tags["61238"].as_str()
 
         meta = meta.strip("'b")
         meta = meta.replace("\\n", "\n")
@@ -81,12 +81,12 @@ def _get_meta_data(path, section, name):
 
     @staticmethod
     def _get_tif(path):
-        if isinstance(path, pathlib.Path):
-            path = str(path)
-        elif not isinstance(path, str):
+        if hasattr(path, "seek"):  # opened file
             # Seek open file zero to avoid error in tifffile:
             # "ValueError: invalid TIFF file"
             path.seek(0)
+        else:  # path
+            path = fspath(path)
         return tifffile.TiffFile(path)
 
     def get_qpimage_raw(self, idx=0):

setup.py

@@ -23,7 +23,8 @@
     license="MIT",
     description=description,
     long_description=open('README.rst').read() if exists('README.rst') else '',
-    install_requires=["nrefocus>=0.1.5",
+    install_requires=["h5py>=2.7.0",
+                      "nrefocus>=0.1.5",
                       "numpy>=1.12.0",
                       "qpimage",
                       "scikit-image>=0.11.0",

tests/test_single_tif_holo.py

@@ -12,7 +12,7 @@ def test_basic():
     # basic tests
     assert ds.storage_type == "hologram"
     assert not ds.is_series
-    assert ds.path == path
+    assert ds.path == path.resolve()
     assert "SingleTifHolo" in ds.__repr__()
 
 

tests/test_single_tif_phasics.py

@@ -51,7 +51,7 @@
 def test_load_data():
     path = datapath / "single_phasics.tif"
     ds = qpformat.load_data(path)
-    assert pathlib.Path(ds.path) == path
+    assert pathlib.Path(ds.path) == path.resolve()
     assert "SingleTifPhasics" in ds.__repr__()