cleanup

qpimage/core.py

@@ -23,7 +23,7 @@
 
 
 class QPImage(object):
-    # required to create in-memory hdf5 files with unique fd
+    # required to create in-memory HDF5 files with unique fd
     _instances = 0
 
     def __init__(self, data=None, bg_data=None, which_data="phase",
@@ -70,7 +70,7 @@ def __init__(self, data=None, bg_data=None, which_data="phase",
                 Previous versions always performed phase unwrapping
                 and did so without offset correction
         h5file: str, pathlib.Path, h5py.Group, h5py.File, or None
-            A path to an hdf5 data file where all data is cached. If
+            A path to an HDF5 data file where all data is cached. If
             set to `None` (default), all data will be handled in
             memory using the "core" driver of the :mod:`h5py`'s
             :class:`h5py:File` class. If the file does not exist,
@@ -385,7 +385,7 @@ def field(self):
 
     @property
     def info(self):
-        """list of tuples with QPImage meta data"""
+        """list of tuples with QPImage metadata"""
         info = []
         # meta data
         meta = self.meta
@@ -561,7 +561,7 @@ def compute_bg(self, which_data="phase",
     def copy(self, h5file=None):
         """Create a copy of the current instance
 
-        This is done by recursively copying the underlying hdf5 data.
+        This is done by recursively copying the underlying HDF5 data.
 
         Parameters
         ----------
@@ -583,13 +583,13 @@ def refocus(self, distance, kernel="helmholtz", padding=True,
         kernel: str
             Refocusing method, one of ["helmholtz","fresnel"]
         padding: bool
-            Whether or not to perform padding during refocusing.
+            Whether to perform padding during refocusing.
             You may disable padding if your input image does not
             have any discontinuities at the border (i.e. you can
-            tile your input image and it would look good), otherwise
+            tile your input image, and it would look good), otherwise
             you will experience ringing artifacts.
         h5file: str, h5py.Group, h5py.File, or None
-            A path to an hdf5 data file where the QPImage is cached.
+            A path to an HDF5 data file where the QPImage is cached.
             If set to `None` (default), all data will be handled in
             memory using the "core" driver of the :mod:`h5py`'s
             :class:`h5py:File` class. If the file does not exist,
@@ -704,18 +704,18 @@ def set_bg_data(self, bg_data, which_data=None, proc_phase=True):
 
 
 def copyh5(inh5, outh5):
-    """Recursively copy all hdf5 data from one group to another
+    """Recursively copy all HDF5 data from one group to another
 
     Data from links is copied.
 
     Parameters
     ----------
     inh5: str, h5py.File, or h5py.Group
-        The input hdf5 data. This can be either a file name or
-        an hdf5 object.
+        The input HDF5 data. This can be either a file name or
+        an HDF5 object.
     outh5: str, h5py.File, h5py.Group, or None
-        The output hdf5 data. This can be either a file name or
-        an hdf5 object. If set to `None`, a new hdf5 object is
+        The output HDF5 data. This can be either a file name or
+        an HDF5 object. If set to `None`, a new HDF5 object is
         created in memory.
 
     Notes
@@ -765,7 +765,7 @@ def copyh5(inh5, outh5):
 
 
 def divmod_neg(a, b):
-    """Return divmod with closest result to zero"""
+    """Return divmod with the closest result to zero"""
     q, r = divmod(a, b)
     # make sure r is close to zero
     sr = np.sign(r)

qpimage/image_data.py

@@ -7,7 +7,7 @@
 
 from . import bg_estimate
 
-#: default hdf5 compression keyword arguments
+#: default HDF5 compression keyword arguments
 COMPRESSION = {"compression": "gzip",
                "compression_opts": 9,
                }
@@ -178,7 +178,7 @@ def estimate_bg(self, fit_offset="mean", fit_profile="tilt",
         intersection of the two resulting mask images is used.
 
         The arguments passed to this method are stored in the
-        hdf5 file `self.h5` and are used for optional integrity
+        HDF5 file `self.h5` and are used for optional integrity
         checking using `qpimage.integrity_check.check`.
 
         See Also
@@ -241,14 +241,14 @@ def get_bg(self, key=None, ret_attrs=False):
                 raise KeyError("No background data for {}!".format(key))
             return ret
 
-    def set_bg(self, bg, key="data", attrs={}):
+    def set_bg(self, bg, key="data", attrs=None):
         """Set the background data
 
         Parameters
         ----------
         bg: numbers.Real, 2d ndarray, ImageData, or h5py.Dataset
             The background data. If `bg` is an `h5py.Dataset` object,
-            it must exist in the same hdf5 file (a hard link is created).
+            it must exist in the same HDF5 file (a hard link is created).
             If set to `None`, the data will be removed.
         key: str
             One of :const:`VALID_BG_KEYS`)
@@ -259,6 +259,8 @@ def set_bg(self, bg, key="data", attrs={}):
         --------
         del_bg: removing background data
         """
+        if attrs is None:
+            attrs = {}
         if key not in VALID_BG_KEYS:
             raise ValueError("Invalid bg key: {}".format(key))
         # remove previous background key
@@ -324,7 +326,7 @@ def _bg_correct(self, raw, bg):
 
 
 def write_image_dataset(group, key, data, h5dtype=None):
-    """Write an image to an hdf5 group as a dataset
+    """Write an image to an HDF5 group as a dataset
 
     This convenience function sets all attributes such that the image
     can be visualized with HDFView, sets the compression and fletcher32
@@ -338,7 +340,7 @@ def write_image_dataset(group, key, data, h5dtype=None):
         Dataset identifier
     data: np.ndarray of shape (M,N)
         Image data to store
-    h5dtype: str
+    h5dtype: str or dtype
         The datatype in which to store the image data. The default
         is the datatype of `data`.
 

qpimage/integrity_check.py

@@ -10,13 +10,13 @@ class IntegrityCheckError(BaseException):
     pass
 
 
-def check(qpi_or_h5file, checks=["attributes", "background"]):
+def check(qpi_or_h5file, checks=None):
     """Checks various properties of a :class:`qpimage.core.QPImage` instance
 
     Parameters
     ----------
     qpi_or_h5file: qpimage.core.QPImage or str
-        A QPImage object or a path to an hdf5 file
+        A QPImage object or a path to an HDF5 file
     checks: list of str
         Which checks to perform ("attributes" and/or "background")
 
@@ -25,7 +25,9 @@ def check(qpi_or_h5file, checks=["attributes", "background"]):
     IntegrityCheckError
         if the checks fail
     """
-    if isinstance(checks, str):
+    if checks is None:
+        checks = ["attributes", "background"]
+    elif isinstance(checks, str):
         checks = [checks]
     for ch in checks:
         if ch not in ["attributes", "background"]:

qpimage/meta.py

@@ -35,7 +35,7 @@
 
 
 class MetaDataMissingError(BaseException):
-    """Raised when meta data is missing"""
+    """Raised when metadata is missing"""
     pass
 
 

qpimage/series.py

@@ -16,13 +16,13 @@ def __init__(self, qpimage_list=[], meta_data={},
         qpimage_list: list
             A list of instances of :class:`qpimage.QPImage`.
         meta_data: dict
-            Meta data associated with the input data
+            Metadata associated with the input data
             (see :const:`qpimage.META_KEYS`). This overrides
-            the meta data of the QPImages in `qpimage_list` and, if
+            the metadata of the QPImages in `qpimage_list` and, if
             `h5file` is given and `h5mode` is not "r", overrides
-            the meta data in `h5file`.
+            the metadata in `h5file`.
         h5file: str, h5py.Group, h5py.File, or None
-            A path to an hdf5 data file where all data is cached. If
+            A path to an HDF5 data file where all data is cached. If
             set to `None` (default), all data will be handled in
             memory using the "core" driver of the :mod:`h5py`'s
             :class:`h5py:File` class. If the file does not exist,
@@ -138,7 +138,7 @@ def add_qpimage(self, qpi, identifier=None, bg_from_idx=None):
             Identifier key for `qpi`
         bg_from_idx: int or None
             Use the background data from the data stored in this index,
-            creating hard links within the hdf5 file.
+            creating hard links within the HDF5 file.
             (Saves memory if e.g. all qpimages is corrected with the same data)
         """
         if not isinstance(qpi, QPImage):
@@ -178,7 +178,7 @@ def get_qpimage(self, index):
         Notes
         -----
         Instead of ``qps.get_qpimage(index)``, it is possible
-        to use the short-hand ``qps[index]``.
+        to use the shorthand ``qps[index]``.
         """
         if isinstance(index, str):
             # search for the identifier