OVerwrite master with current stable to restart dev 0.11 tree

.gitignore

@@ -51,7 +51,3 @@ Backup_of_*.cdr
 
 #Profuling
 prof
-
-#LockFiles
-*.dirlock
-*.lock

README.rst

@@ -41,7 +41,8 @@ Getting this Code
     :alt: Introduction and Installation Guide to Stoner Pythin Package
     :width: 320
 
-See the `requirements.txt` file for the current package requirements.
+The *Stoner* package requires h5py>=2.7.0, lmfit>=0.9.7, matplotlib>=2.0,numpy>=1.13, Pillow>=4.0,
+scikit-image>=0.13.0 & scipy>=1.0.0 and also optional depends on  filemagic, npTDMS, imreg_dft and numba, fabio, hyperspy.
 
 Ananconda Python (and probably other scientific Python distributions) include nearly all of the dependencies, and the remaining
 dependencies are collected together in the **phygbu** repositry on anaconda cloud. The easiest way to install the Stoner package is,
@@ -50,10 +51,10 @@ therefore, to install the most recent Anaconda Python distribution.
 Compatibility
 --------------
 
-Versions 0.10.x (stable branch) are compatible with Python 3.6-3.9. The current development branch is targetting v3.8-3.9
-with 3.10 added when anaconda support is available in mainstream realease.
+Versions 0.9.x (stable branch) are compatible with Python 2.7, 3.5, 3.6 and 3.7. The latest 0.9.6 version is also compatible with Python 3.8
+The current stable verstion (0.10, stable branch) is compatible with Python 3.6-3.9
 
-Conda packages are built on each github release via a github actions for 64bit Python on Windows, MacOS and Linux.
+Conda packages are prepared for the stable branch and when the development branch enters beta testing. Pip wheels are prepared for selected stable releases only.
 
 Installation
 ------------

Stoner/Analysis.py

@@ -1,12 +1,17 @@
 """Stoner .Analysis provides a subclass of :class:`.Data` that has extra analysis routines builtin."""
 
-__all__ = ["AnalysisMixin"]
+__all__ = ["AnalysisMixin", "GetAffineTransform", "ApplyAffineTransform"]
+from inspect import getfullargspec
 import numpy as np
 import numpy.ma as ma
 
 from scipy.integrate import cumtrapz
+from scipy.optimize import curve_fit
 
 from .tools import isiterable, isTuple
+from .compat import string_types
+from .core.exceptions import assertion
+from .analysis.utils import threshold as _threshold, ApplyAffineTransform, GetAffineTransform
 
 # from matplotlib.pylab import * #Surely not?
 

Stoner/Core.py

@@ -30,7 +30,7 @@
 
 from .compat import string_types, int_types, index_types, _pattern_type, path_types
 from .tools import all_type, isiterable, isLikeList, get_option, make_Data
-from .tools.file import get_file_name_type, auto_load_classes, get_file_type
+from .tools.file import get_file_name_type, auto_load_classes
 
 from .core.exceptions import StonerLoadError, StonerSetasError
 from .core import _setas, regexpDict, typeHintedDict, metadataObject
@@ -1369,8 +1369,6 @@ def load(cls, *args, **kargs):
             filename, filetype = get_file_name_type(filename, filetype, DataFile)
         elif not auto_load and not filetype:
             raise StonerLoadError("Cannot read data from non-path like filenames !")
-        else:
-            filetype = get_file_type(filetype, DataFile)
         if auto_load:  # We're going to try every subclass we canA
             ret = auto_load_classes(filename, DataFile, debug=False, args=args, kargs=kargs)
             if not isinstance(ret, DataFile):  # autoload returned something that wasn't a data file!

Stoner/HDF5.py

@@ -3,7 +3,7 @@
 Classes include
 
 * HDF5File - A :py:class:`Stoner.Code.DataFile` subclass that can save and load data from hdf5 files
-* HDF5Folder - A :py:class:`Stoner.folders.DataFolder` subclass that can save and load data from a single hdf5 file
+* HDF5Folder - A :py:class:`Stoner.Folders.DataFolder` subclass that can save and load data from a single hdf5 file
 
 It is only necessary to import this module for the subclasses of :py:class:`Stoner.Core.DataFile` to become available
 to :py:class:`Stoner.Core.Data`.
@@ -375,7 +375,7 @@ class HDF5FolderMixin:
 
     """Provides a method to load and save data from a single HDF5 file with groups.
 
-    See :py:class:`Stoner.folders.DataFolder` for documentation on constructor.
+    See :py:class:`Stoner.Folders.DataFolder` for documentation on constructor.
 
     Datalayout consistns of sub-groups that are either instances of HDF5Files (i.e. have a type attribute that
     contains 'HDF5File') or are themsleves HDF5Folder instances (with a type attribute that reads 'HDF5Folder').

Stoner/Image/core.py

@@ -8,7 +8,7 @@
 from io import BytesIO as StreamIO
 from warnings import warn
 
-from PIL import Image, PngImagePlugin
+from PIL import Image
 import numpy as np
 import matplotlib.pyplot as plt
 from scipy import ndimage as ndi
@@ -26,6 +26,7 @@
     segmentation,
     transform,
 )
+
 from ..core.base import typeHintedDict, metadataObject
 from ..core.exceptions import StonerLoadError, StonerUnrecognisedFormat
 from ..Core import DataFile
@@ -37,18 +38,12 @@
     get_filedialog,
     int_types,
     path_types,
-    str2bytes,
 )  # Some things to help with Python2 and Python3 compatibility
 from .attrs import DrawProxy, MaskProxy
 from .widgets import RegionSelect
 from . import imagefuncs
 from ..tools.classes import Options
 
-if "READTHEDOCS" not in os.environ:
-    from skimage import viewer
-else:
-    from ..tools import null as viewer
-
 IMAGE_FILES = [("Tiff File", "*.tif;*.tiff"), ("PNG files", "*.png", "Numpy Files", "*.npy")]
 
 dtype_range = {

Stoner/Image/folders.py

@@ -13,7 +13,7 @@
 from PIL import Image
 
 from .core import ImageArray
-from ..folders import DiskBasedFolderMixin, baseFolder
+from ..Folders import DiskBasedFolderMixin, baseFolder
 from ..compat import string_types, int_types
 from . import ImageFile
 
@@ -366,7 +366,7 @@ def montage(self, *args, **kargs):
             else:
                 j += 1
             fig = figure(fignum)
-            ax = fig.add_subplot(plt_y, plt_x, j)
+            ax = subplot(plt_y, plt_x, j)
             plt_kargs["figure"] = fig
             plt_kargs["ax"] = ax
             if "title" in kargs:

Stoner/Image/stack.py

@@ -9,7 +9,7 @@
 from ..core.exceptions import assertion
 
 from ..Core import regexpDict, typeHintedDict
-from ..folders import DiskBasedFolderMixin, baseFolder
+from ..Folders import DiskBasedFolderMixin, baseFolder
 
 from .core import ImageArray, ImageFile
 from .folders import ImageFolder, ImageFolderMixin

Stoner/Util.py

@@ -171,8 +171,8 @@ def split_up_down(data, col=None, folder=None):
             object containign the data to be sorted
         col (index):
             is something that :py:meth:`Stoner.Core.DataFile.find_col` can use
-        folder (:py:class:`Stoner.folders.DataFolder` or None):
-            if this is an instance of :py:class:`Stoner.folders.DataFolder` then add
+        folder (:py:class:`Stoner.Folders.DataFolder` or None):
+            if this is an instance of :py:class:`Stoner.Folders.DataFolder` then add
             rising and falling files to groups of this DataFolder, otherwise create a new one
 
     Returns:

Stoner/Zip.py

@@ -4,7 +4,7 @@
 Classes Include
 
 * ZippedFile - A :py:class:`Stoner.Code.DataFile` subclass that can save and load data from a zip files
-* ZipFolder - A :py:class:`Stoner.folders.DataFolder` subclass that can save and load data from a single zip file
+* ZipFolder - A :py:class:`Stoner.Folders.DataFolder` subclass that can save and load data from a single zip file
 """
 __all__ = ["test_is_zip", "ZippedFile", "ZipFolderMixin", "ZipFolder"]
 import zipfile as zf
@@ -14,7 +14,7 @@
 
 from .compat import string_types, str2bytes, get_filedialog, _pattern_type, path_types
 from .Core import DataFile, StonerLoadError
-from .folders import DiskBasedFolderMixin
+from .Folders import DiskBasedFolderMixin
 from .folders.core import baseFolder
 from .folders.utils import pathjoin
 from .tools import copy_into, make_Data
@@ -231,7 +231,7 @@ class ZipFolderMixin:
 
     """Provides methods to load and save data from a single Zip file.
 
-    See :py:class:`Stoner.folders.DataFolder` for documentation on constructor.
+    See :py:class:`Stoner.Folders.DataFolder` for documentation on constructor.
 
     Note:
         As this mixin class provides both read and write storage, it cannot be mixed in with another class that
@@ -492,7 +492,7 @@ def _save(self, f, trail):
         :py:meth:`Stoner.Zip.ZipFile.save`
 
         This routine is used by a walk_groups call - hence the prototype matches that required for
-        :py:meth:`Stoner.folders.DataFolder.walk_groups`.
+        :py:meth:`Stoner.Folders.DataFolder.walk_groups`.
 
         """
         if not isinstance(f, DataFile):

Stoner/__init__.py

@@ -27,7 +27,7 @@
 
 from . import core, analysis, formats, plot, tools, Image
 from .core.data import Data
-from .folders import DataFolder
+from .Folders import DataFolder
 from .Image import ImageFile, ImageFolder, ImageStack
 
 from .tools import set_option, get_option, Options as _Options