ref: restructure file_format submodule

qpformat/file_formats/__init__.py

@@ -2,8 +2,9 @@
 from os.path import commonprefix
 import pathlib
 
-from .dataset import SeriesData, hash_obj
-from .dataset import SingleData  # noqa:F401 (user convenience)
+from .series_base import SeriesData
+from .single_base import SingleData  # noqa:F401 (user convenience)
+from .util import hash_obj
 from . import fmts_ready, fmts_raw_oah
 
 

qpformat/file_formats/fmts_raw_oah/series_hdf5_hyperspy.py

@@ -4,7 +4,7 @@
 import h5py
 import qpimage
 
-from ..dataset import SeriesData
+from ..series_base import SeriesData
 
 
 class HyperSpyNoDataFoundError(BaseException):

qpformat/file_formats/fmts_raw_oah/series_hdf5_raw_oah.py

@@ -5,7 +5,7 @@
 import numpy as np
 import qpimage
 
-from ..dataset import SeriesData
+from ..series_base import SeriesData
 
 
 class SeriesHDF5RawOAH(SeriesData):

qpformat/file_formats/fmts_raw_oah/series_zip_tif_holo.py

@@ -5,7 +5,8 @@
 
 import numpy as np
 
-from ..dataset import SeriesData
+from ..series_base import SeriesData
+
 from .single_tif_holo import SingleTifHolo
 
 

qpformat/file_formats/fmts_raw_oah/single_hdf5_raw_oah.py

@@ -4,7 +4,7 @@
 import numpy as np
 import qpimage
 
-from ..dataset import SingleData
+from ..single_base import SingleData
 
 
 class SingleHDF5RawOAH(SingleData):

qpformat/file_formats/fmts_raw_oah/single_tif_holo.py

@@ -6,7 +6,7 @@
 import qpimage
 import tifffile
 
-from ..dataset import SingleData
+from ..single_base import SingleData
 
 
 class SingleTifHolo(SingleData):

qpformat/file_formats/fmts_ready/series_hdf5_meep.py

@@ -5,7 +5,7 @@
 import numpy as np
 import qpimage
 
-from ..dataset import SeriesData
+from ..series_base import SeriesData
 
 
 class NoSinogramDataFoundError(BaseException):

qpformat/file_formats/fmts_ready/series_hdf5_qpimage.py

@@ -1,7 +1,7 @@
 import h5py
 import qpimage
 
-from ..dataset import SeriesData
+from ..series_base import SeriesData
 
 
 class SeriesHdf5Qpimage(SeriesData):

qpformat/file_formats/fmts_ready/series_zip_tif_phasics.py

@@ -2,7 +2,7 @@
 import functools
 import zipfile
 
-from ..dataset import SeriesData
+from ..series_base import SeriesData
 from .single_tif_phasics import SingleTifPhasics
 
 

qpformat/file_formats/fmts_ready/single_hdf5_qpimage.py

@@ -1,7 +1,7 @@
 import h5py
 import qpimage
 
-from ..dataset import SingleData
+from ..single_base import SingleData
 
 
 class SingleHdf5Qpimage(SingleData):

qpformat/file_formats/fmts_ready/single_npy_numpy.py

@@ -5,7 +5,7 @@
 import numpy as np
 import qpimage
 
-from ..dataset import SingleData
+from ..single_base import SingleData
 
 
 class SingleNpyNumpy(SingleData):

qpformat/file_formats/fmts_ready/single_tif_phasics.py

@@ -8,7 +8,7 @@
 import qpimage
 import tifffile
 
-from ..dataset import SingleData
+from ..single_base import SingleData
 
 
 # baseline clamp intensity normalization for phasics tif files

qpformat/file_formats/dataset.py → qpformat/file_formats/series_base.py

@@ -1,13 +1,14 @@
 import abc
 import copy
 import functools
-import hashlib
 import io
 import pathlib
 
 import numpy as np
 import qpimage
 
+from .util import hash_obj
+
 
 class SeriesData(object):
     """Series data file format base class
@@ -353,74 +354,3 @@ def verify(path):
         memory efficient, because e.g. the "GroupFolder" file
         format depends on it.
         """
-
-
-class SingleData(SeriesData):
-    """Single data file format base class
-
-    Parameters
-    ----------
-    path: str or pathlib.Path
-        Path to the experimental data file.
-    meta_data: dict
-        Dictionary containing meta data.
-        see :py:class:`qpimage.META_KEYS`.
-    as_type: str
-        Defines the data type that the input data is casted to.
-        The default is "float32" which saves memory. If high
-        numerical accuracy is required (does not apply for a
-        simple 2D phase analysis), set this to double precision
-        ("float64").
-    """
-    __meta__ = abc.ABCMeta
-    is_series = False
-
-    def __len__(self):
-        return 1
-
-    def get_identifier(self, idx=0):
-        return self.identifier
-
-    def get_name(self, idx=0):
-        return super(SingleData, self).get_name(idx=0)
-
-    def get_qpimage(self, idx=0):
-        return super(SingleData, self).get_qpimage(idx=0)
-
-    @abc.abstractmethod
-    def get_qpimage_raw(self, idx=0):
-        """QPImage without background correction"""
-
-    def get_time(self, idx=0):
-        """Time of the data
-
-        Returns nan if the time is not defined
-        """
-        thetime = super(SingleData, self).get_time(idx=0)
-        return thetime
-
-
-def hash_obj(data, maxlen=5):
-    hasher = hashlib.md5()
-    tohash = obj2bytes(data)
-    hasher.update(tohash)
-    return hasher.hexdigest()[:maxlen]
-
-
-def obj2bytes(data):
-    tohash = []
-    if isinstance(data, (tuple, list)):
-        for item in data:
-            tohash.append(obj2bytes(item))
-    elif isinstance(data, str):
-        tohash.append(data.encode("utf-8"))
-    elif isinstance(data, bytes):
-        tohash.append(data)
-    elif isinstance(data, np.ndarray):
-        tohash.append(data.tobytes())
-    elif isinstance(data, int):
-        tohash.append(bytes(data))
-    else:
-        msg = "No rule to convert to bytes: {}".format(data)
-        raise NotImplementedError(msg)
-    return b"".join(tohash)

qpformat/file_formats/single_base.py

@@ -0,0 +1,48 @@
+import abc
+
+from .series_base import SeriesData
+
+
+class SingleData(SeriesData):
+    """Single data file format base class
+
+    Parameters
+    ----------
+    path: str or pathlib.Path
+        Path to the experimental data file.
+    meta_data: dict
+        Dictionary containing meta data.
+        see :py:class:`qpimage.META_KEYS`.
+    as_type: str
+        Defines the data type that the input data is casted to.
+        The default is "float32" which saves memory. If high
+        numerical accuracy is required (does not apply for a
+        simple 2D phase analysis), set this to double precision
+        ("float64").
+    """
+    __meta__ = abc.ABCMeta
+    is_series = False
+
+    def __len__(self):
+        return 1
+
+    def get_identifier(self, idx=0):
+        return self.identifier
+
+    def get_name(self, idx=0):
+        return super(SingleData, self).get_name(idx=0)
+
+    def get_qpimage(self, idx=0):
+        return super(SingleData, self).get_qpimage(idx=0)
+
+    @abc.abstractmethod
+    def get_qpimage_raw(self, idx=0):
+        """QPImage without background correction"""
+
+    def get_time(self, idx=0):
+        """Time of the data
+
+        Returns nan if the time is not defined
+        """
+        thetime = super(SingleData, self).get_time(idx=0)
+        return thetime

qpformat/file_formats/util.py

@@ -0,0 +1,29 @@
+import hashlib
+
+import numpy as np
+
+
+def hash_obj(data, maxlen=5):
+    hasher = hashlib.md5()
+    tohash = obj2bytes(data)
+    hasher.update(tohash)
+    return hasher.hexdigest()[:maxlen]
+
+
+def obj2bytes(data):
+    tohash = []
+    if isinstance(data, (tuple, list)):
+        for item in data:
+            tohash.append(obj2bytes(item))
+    elif isinstance(data, str):
+        tohash.append(data.encode("utf-8"))
+    elif isinstance(data, bytes):
+        tohash.append(data)
+    elif isinstance(data, np.ndarray):
+        tohash.append(data.tobytes())
+    elif isinstance(data, int):
+        tohash.append(bytes(data))
+    else:
+        msg = "No rule to convert to bytes: {}".format(data)
+        raise NotImplementedError(msg)
+    return b"".join(tohash)

tests/requirements.txt

@@ -0,0 +1 @@
+pytest