Updated to work with Python 3!

GUIs now import .ui-files directly.

Updated to work with Python 3!
51b39c56 · Jan Caron · d2eef42e · 51b39c56 · d2eef42e · d2eef42e
Commit 51b39c56 authored 8 years ago by Jan Caron
--- a/.hgignore
+++ b/.hgignore
@@ -13,3 +13,4 @@ files*
 build*
 Pyramid.egg-info*
 logfile.log
+.idea*
--- a/.idea/.name
+++ b/.idea/.name
-Pyramid
\ No newline at end of file
--- a/.idea/Pyramid.iml
+++ b/.idea/Pyramid.iml
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/pyramid" isTestSource="false" />
-    </content>
-    <orderEntry type="jdk" jdkName="Python 2.7.11 (C:\Anaconda2\python.exe)" jdkType="Python SDK" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="HyperSpy" />
-    <orderEntry type="module" module-name="Jutil" />
-    <orderEntry type="module" module-name="Publications" />
-    <orderEntry type="module" module-name="Script-Vault" />
-  </component>
-  <component name="ReSTService">
-    <option name="workdir" value="$MODULE_DIR$" />
-    <option name="DOC_DIR" value="$MODULE_DIR$" />
-  </component>
-  <component name="TestRunnerService">
-    <option name="projectConfiguration" value="Nosetests" />
-    <option name="PROJECT_TEST_RUNNER" value="Nosetests" />
-  </component>
-</module>
\ No newline at end of file
--- a/.idea/codeStyleSettings.xml
+++ b/.idea/codeStyleSettings.xml
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectCodeStyleSettingsManager">
-    <option name="PER_PROJECT_SETTINGS">
-      <value>
-        <XML>
-          <option name="XML_LEGACY_SETTINGS_IMPORTED" value="true" />
-        </XML>
-      </value>
-    </option>
-    <option name="PREFERRED_PROJECT_CODE_STYLE" value="Default (1)" />
-  </component>
-</project>
\ No newline at end of file
--- a/.idea/dictionaries/Jan.xml
+++ b/.idea/dictionaries/Jan.xml
-<component name="ProjectDictionaryState">
-  <dictionary name="Jan" />
-</component>
\ No newline at end of file
--- a/.idea/encodings.xml
+++ b/.idea/encodings.xml
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="Encoding">
-    <file url="PROJECT" charset="UTF-8" />
-  </component>
-</project>
\ No newline at end of file
--- a/.idea/inspectionProfiles/Project_Default.xml
+++ b/.idea/inspectionProfiles/Project_Default.xml
-<component name="InspectionProjectProfileManager">
-  <profile version="1.0">
-    <option name="myName" value="Project Default" />
-    <inspection_tool class="LongLine" enabled="true" level="WARNING" enabled_by_default="true">
-      <scope name="*.c" level="WARNING" enabled="false" />
-    </inspection_tool>
-    <inspection_tool class="PyArgumentListInspection" enabled="true" level="WARNING" enabled_by_default="true">
-      <scope name="gui" level="WARNING" enabled="false" />
-    </inspection_tool>
-    <inspection_tool class="PyAttributeOutsideInitInspection" enabled="false" level="WEAK WARNING" enabled_by_default="false" />
-    <inspection_tool class="PyBroadExceptionInspection" enabled="false" level="WEAK WARNING" enabled_by_default="false" />
-    <inspection_tool class="PyCallByClassInspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
-      <scope name="gui" level="WEAK WARNING" enabled="false" />
-    </inspection_tool>
-    <inspection_tool class="PyClassicStyleClassInspection" enabled="true" level="WARNING" enabled_by_default="true">
-      <scope name="gui" level="WARNING" enabled="false" />
-    </inspection_tool>
-    <inspection_tool class="PyCompatibilityInspection" enabled="true" level="WARNING" enabled_by_default="true">
-      <option name="ourVersions">
-        <value>
-          <list size="1">
-            <item index="0" class="java.lang.String" itemvalue="3.5" />
-          </list>
-        </value>
-      </option>
-    </inspection_tool>
-    <inspection_tool class="PyMandatoryEncodingInspection" enabled="true" level="WARNING" enabled_by_default="true" />
-    <inspection_tool class="PyMissingOrEmptyDocstringInspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
-      <scope name="gui" level="WEAK WARNING" enabled="false" />
-    </inspection_tool>
-    <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
-      <scope name="gui" level="WARNING" enabled="false">
-        <option name="ignoredPackages">
-          <value>
-            <list size="0" />
-          </value>
-        </option>
-      </scope>
-      <scope name="scripts" level="WARNING" enabled="true">
-        <option name="ignoredPackages">
-          <value>
-            <list size="2">
-              <item index="0" class="java.lang.String" itemvalue="pylab" />
-              <item index="1" class="java.lang.String" itemvalue="tqdm" />
-            </list>
-          </value>
-        </option>
-      </scope>
-      <option name="ignoredPackages">
-        <value>
-          <list size="1">
-            <item index="0" class="java.lang.String" itemvalue="hyperspy" />
-          </list>
-        </value>
-      </option>
-    </inspection_tool>
-    <inspection_tool class="PyPep8Inspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
-      <scope name="__init__" level="WEAK WARNING" enabled="true">
-        <option name="ignoredErrors">
-          <list>
-            <option value="E402" />
-          </list>
-        </option>
-      </scope>
-      <option name="ignoredErrors">
-        <list>
-          <option value="W503" />
-        </list>
-      </option>
-    </inspection_tool>
-    <inspection_tool class="PyPep8NamingInspection" enabled="false" level="WEAK WARNING" enabled_by_default="false" />
-    <inspection_tool class="PyShadowingNamesInspection" enabled="false" level="WEAK WARNING" enabled_by_default="false" />
-    <inspection_tool class="PyTypeCheckerInspection" enabled="false" level="WARNING" enabled_by_default="false" />
-    <inspection_tool class="PyUnresolvedReferencesInspection" enabled="true" level="WARNING" enabled_by_default="true">
-      <scope name="__init__" level="WARNING" enabled="false" />
-      <option name="ignoredIdentifiers">
-        <list>
-          <option value="multiprocessing" />
-          <option value="hyperspy.api" />
-        </list>
-      </option>
-    </inspection_tool>
-    <inspection_tool class="SpellCheckingInspection" enabled="false" level="TYPO" enabled_by_default="false">
-      <option name="processCode" value="true" />
-      <option name="processLiterals" value="true" />
-      <option name="processComments" value="true" />
-    </inspection_tool>
-    <inspection_tool class="TodoComment" enabled="false" level="INFO" enabled_by_default="false" />
-  </profile>
-</component>
\ No newline at end of file
--- a/.idea/inspectionProfiles/profiles_settings.xml
+++ b/.idea/inspectionProfiles/profiles_settings.xml
-<component name="InspectionProjectProfileManager">
-  <settings>
-    <option name="PROJECT_PROFILE" value="Project Default" />
-    <option name="USE_PROJECT_PROFILE" value="true" />
-    <version value="1.0" />
-  </settings>
-</component>
\ No newline at end of file
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectLevelVcsManager" settingsEditedManually="false">
-    <OptionsSetting value="true" id="Add" />
-    <OptionsSetting value="true" id="Remove" />
-    <OptionsSetting value="true" id="Checkout" />
-    <OptionsSetting value="true" id="Update" />
-    <OptionsSetting value="true" id="Status" />
-    <OptionsSetting value="true" id="Edit" />
-    <ConfirmationsSetting value="0" id="Add" />
-    <ConfirmationsSetting value="0" id="Remove" />
-  </component>
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 2.7.11 (C:\Anaconda2\python.exe)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file
--- a/.idea/modules.xml
+++ b/.idea/modules.xml
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/../HyperSpy/.idea/HyperSpy.iml" filepath="$PROJECT_DIR$/../HyperSpy/.idea/HyperSpy.iml" />
-      <module fileurl="file://$PROJECT_DIR$/../Jutil/.idea/Jutil.iml" filepath="$PROJECT_DIR$/../Jutil/.idea/Jutil.iml" />
-      <module fileurl="file://$PROJECT_DIR$/../Publications/.idea/Publications.iml" filepath="$PROJECT_DIR$/../Publications/.idea/Publications.iml" />
-      <module fileurl="file://$PROJECT_DIR$/.idea/Pyramid.iml" filepath="$PROJECT_DIR$/.idea/Pyramid.iml" />
-      <module fileurl="file://$PROJECT_DIR$/../Script-Vault/.idea/Script-Vault.iml" filepath="$PROJECT_DIR$/../Script-Vault/.idea/Script-Vault.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file
--- a/.idea/scopes/__c.xml
+++ b/.idea/scopes/__c.xml
-<component name="DependencyValidationManager">
-  <scope name="*.c" pattern="file[Pyramid]:pyramid/numcore/*.c" />
-</component>
\ No newline at end of file
--- a/.idea/scopes/__init__.xml
+++ b/.idea/scopes/__init__.xml
-<component name="DependencyValidationManager">
-  <scope name="__init__" pattern="file[Pyramid]:pyramid/__init__.py" />
-</component>
\ No newline at end of file
--- a/.idea/vcs.xml
+++ b/.idea/vcs.xml
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="VcsDirectoryMappings">
-    <mapping directory="" vcs="hg4idea" />
-    <mapping directory="$PROJECT_DIR$/../Jutil" vcs="hg4idea" />
-    <mapping directory="$PROJECT_DIR$/../Publications" vcs="hg4idea" />
-    <mapping directory="$PROJECT_DIR$/../Script-Vault" vcs="hg4idea" />
-  </component>
-</project>
\ No newline at end of file
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
--- a/pyramid/__init__.py
+++ b/pyramid/__init__.py
@@ -48,13 +48,6 @@ numcore

 """

-import logging
-_log = logging.getLogger(__name__)
-try:  # Try importing HyperSpy (here because otherwise API Errors might occur):
-    import hyperspy.api
-except ImportError:
-    _log.error('Could not load hyperspy package!')
-
 from . import analytic
 from . import magcreator
 from . import reconstruction
@@ -92,6 +85,8 @@ from .config import *
 from .version import version as __version__
 from .version import hg_revision as __hg_revision__

+import logging
+_log = logging.getLogger(__name__)
 _log.info("Starting Pyramid V{} HG{}".format(__version__, __hg_revision__))
 del logging


--- a/pyramid/colormap.py
+++ b/pyramid/colormap.py
@@ -83,7 +83,7 @@ class DirectionalColormap(colors.LinearSegmentedColormap):
    def __init__(self, inverted=False):
        self._log.debug('Calling __create_directional_colormap')
        cdict = self.CDICT_INV if inverted else self.CDICT
-        super(DirectionalColormap, self).__init__('directional_colormap', cdict, N=256)
+        super().__init__('directional_colormap', cdict, N=256)
        self._log.debug('Created ' + str(self))

    @classmethod
@@ -250,5 +250,5 @@ class TransparentColormap(colors.LinearSegmentedColormap):
        blue = [(0., 0., b), (1., b, 1.)]
        alpha = [(0., 0., alpha_range[0]), (1., alpha_range[1], 1.)]
        cdict = {'red': red, 'green': green, 'blue': blue, 'alpha': alpha}
-        super(TransparentColormap, self).__init__('transparent_colormap', cdict, N=256)
+        super().__init__('transparent_colormap', cdict, N=256)
        self._log.debug('Created ' + str(self))
--- a/pyramid/fft.py
+++ b/pyramid/fft.py
@@ -11,10 +11,8 @@ FFT operations.

 """

-try:
-    import cPickle as pickle
-except ImportError:
-    import pickle
+
+import pickle
 import logging
 import os

@@ -22,28 +20,19 @@ import numpy as np

 from pyramid.config import NTHREADS

-# pyFFTW depends on this
-# try:
-#     from collections import Counter
-# except ImportError:
-#     from collections_python27 import Counter
-#     import collections
-#
-#     collections.Counter = Counter
+_log = logging.getLogger(__name__)

 try:
    import pyfftw
-
    BACKEND = 'fftw'
 except ImportError:
    pyfftw = None
    BACKEND = 'numpy'
-    print("pyFFTW module not found. Using numpy implementation.")
+    _log.info('pyFFTW module not found. Using numpy implementation.')

 __all__ = ['PLANS', 'FLOAT', 'COMPLEX', 'dump_wisdom', 'load_wisdom',  # analysis:ignore
           'zeros', 'empty', 'configure_backend',
           'fftn', 'ifftn', 'rfftn', 'irfftn', 'rfftn_adj', 'irfftn_adj']
-_log = logging.getLogger(__name__)


 class FFTWCache(object):
@@ -384,6 +373,12 @@ def configure_backend(backend):


 # On import:
+ifftn = None
+fftn = None
+rfftn = None
+irfftn = None
+rfftn_adj = None
+irfftn_adj = None
 if pyfftw is not None:
    configure_backend('fftw')
 else:

--- a/pyramid/fielddata.py
+++ b/pyramid/fielddata.py
@@ -6,19 +6,18 @@

 from __future__ import division

-from scipy.ndimage.interpolation import zoom
-
-from pyramid import fft
-from pyramid.colormap import DirectionalColormap
-
+import abc
 import logging
 import os
-from abc import ABCMeta, abstractmethod
 from numbers import Number

 import numpy as np
 from matplotlib import pyplot as plt
 from matplotlib.ticker import MaxNLocator
+from scipy.ndimage.interpolation import zoom
+
+from pyramid import fft
+from pyramid.colormap import DirectionalColormap

 _log = logging.getLogger(__name__)
 try:  # Try importing HyperSpy:
@@ -30,7 +29,7 @@ except ImportError:
 __all__ = ['VectorData', 'ScalarData']


-class FieldData(object):
+class FieldData(object, metaclass=abc.ABCMeta):
    """Class for storing field data.

    Abstract base class for the representatio of magnetic or electric fields (see subclasses).
@@ -50,7 +49,6 @@ class FieldData(object):

    """

-    __metaclass__ = ABCMeta
    _log = logging.getLogger(__name__ + '.FieldData')

    @property
@@ -231,7 +229,7 @@ class FieldData(object):
        mlab.orientation_axes()
        return plot

-    @abstractmethod
+    @abc.abstractmethod
    def scale_down(self, n):
        """Scale down the field distribution by averaging over two pixels along each axis.

@@ -252,7 +250,7 @@ class FieldData(object):
        """
        pass

-    @abstractmethod
+    @abc.abstractmethod
    def scale_up(self, n, order):
        """Scale up the field distribution using spline interpolation of the requested order.

@@ -275,7 +273,7 @@ class FieldData(object):
        """
        pass

-    @abstractmethod
+    @abc.abstractmethod
    def get_vector(self, mask):
        """Returns the field as a vector, specified by a mask.

@@ -292,7 +290,7 @@ class FieldData(object):
        """
        pass

-    @abstractmethod
+    @abc.abstractmethod
    def set_vector(self, vector, mask):
        """Set the field of the masked pixels to the values specified by `vector`.

@@ -310,7 +308,7 @@ class FieldData(object):
        """
        pass

-    @abstractmethod
+    @abc.abstractmethod
    def to_signal(self):
        """Convert :class:`~.FieldData` data into a HyperSpy signal.

@@ -326,7 +324,7 @@ class FieldData(object):
        """
        pass

-    @abstractmethod
+    @abc.abstractmethod
    def save_to_hdf5(self, filename, *args, **kwargs):
        """Save field data in a file with HyperSpys HDF5-format.

@@ -365,11 +363,6 @@ class VectorData(FieldData):
    """
    _log = logging.getLogger(__name__ + '.VectorData')

-    def __init__(self, a, field):
-        self._log.debug('Calling __init__')
-        super(VectorData, self).__init__(a, field)
-        self._log.debug('Created ' + str(self))
-
    def scale_down(self, n=1):
        """Scale down the field distribution by averaging over two pixels along each axis.

@@ -389,7 +382,7 @@ class VectorData(FieldData):

        """
        self._log.debug('Calling scale_down')
-        assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
+        assert n > 0 and isinstance(n, int), 'n must be a positive integer!'
        self.a *= 2 ** n
        for t in range(n):
            # Pad if necessary:
@@ -422,8 +415,8 @@ class VectorData(FieldData):
        Acts in place and changes dimensions and grid spacing accordingly.
        """
        self._log.debug('Calling scale_up')
-        assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
-        assert 5 > order >= 0 and isinstance(order, (int, long)), \
+        assert n > 0 and isinstance(n, int), 'n must be a positive integer!'
+        assert 5 > order >= 0 and isinstance(order, int), \
            'order must be a positive integer between 0 and 5!'
        self.a /= 2 ** n
        self.field = np.array((zoom(self.field[0], zoom=2 ** n, order=order),
@@ -1056,11 +1049,6 @@ class ScalarData(FieldData):
    """
    _log = logging.getLogger(__name__ + '.ScalarData')

-    def __init__(self, a, field):
-        self._log.debug('Calling __init__')
-        super(ScalarData, self).__init__(a, field)
-        self._log.debug('Created ' + str(self))
-
    def scale_down(self, n=1):
        """Scale down the field distribution by averaging over two pixels along each axis.

@@ -1080,7 +1068,7 @@ class ScalarData(FieldData):

        """
        self._log.debug('Calling scale_down')
-        assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
+        assert n > 0 and isinstance(n, int), 'n must be a positive integer!'
        self.a *= 2 ** n
        for t in range(n):
            # Pad if necessary:
@@ -1112,8 +1100,8 @@ class ScalarData(FieldData):
        Acts in place and changes dimensions and grid spacing accordingly.
        """
        self._log.debug('Calling scale_up')
-        assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
-        assert 5 > order >= 0 and isinstance(order, (int, long)), \
+        assert n > 0 and isinstance(n, int), 'n must be a positive integer!'
+        assert 5 > order >= 0 and isinstance(order, int), \
            'order must be a positive integer between 0 and 5!'
        self.a /= 2 ** n
        self.field = zoom(self.field, zoom=2 ** n, order=order)

--- a/pyramid/forwardmodel.py
+++ b/pyramid/forwardmodel.py
@@ -5,7 +5,7 @@
 """This module provides the :class:`~.ForwardModel` class which represents a strategy to map a
 threedimensional magnetization distribution onto a two-dimensional phase map."""

-from __future__ import division, print_function
+from __future__ import division

 import logging
 import multiprocessing as mp
@@ -188,7 +188,7 @@ class DistributedForwardModel(ForwardModel):

    def __init__(self, data_set, ramp_order=None, nprocs=1):
        # Evoke super constructor to set up the normal ForwardModel:
-        super(DistributedForwardModel, self).__init__(data_set, ramp_order)
+        super().__init__(data_set, ramp_order)
        # Initialize multirocessing specific stuff:
        self.nprocs = nprocs
        img_per_proc = np.ceil(self.data_set.count / self.nprocs).astype(np.int)

--- a/pyramid/kernel.py
+++ b/pyramid/kernel.py
@@ -5,8 +5,6 @@
 """This module provides the :class:`~.Kernel` class, representing the phase contribution of one
 single magnetized pixel."""

-from __future__ import print_function
-
 import logging

 import numpy as np
@@ -89,6 +87,10 @@ class Kernel(object):
        self.slice_mag = (slice(0, dim_uv[0]),  # Magnetization is padded on the far end!
                          slice(0, dim_uv[1]))  # (Phase cutout is shifted as listed above)
        # Calculate kernel (single pixel phase):
+        # [M_0] = [PHI_0 / µ_0] = Tm² / N/A² = N/Am * A²/N = A/m
+        #       --> This is the magnetization, not the magnetic moment (A/m * m³ = Am²)!
+        # [b_0] = [µ_0] * [M_0] = A/m * N/A² = N/Am = T
+        # [coeff] = [b_0 * a² / (2*PHI_0)] = T * m² / Tm² = 1  --> without unit (phase)!
        coeff = b_0 * a ** 2 / (2 * PHI_0)  # Minus is gone because of negative z-direction
        v_dim, u_dim = dim_uv
        u = np.linspace(-(u_dim - 1), u_dim - 1, num=2 * u_dim - 1)
@@ -141,7 +143,7 @@ class Kernel(object):
        None

        """
-        self._log.debug('Calling print_info')
+        self._log.debug('Calling log_info')
        print('Shape of the FOV   :', self.dim_uv)
        print('Shape of the Kernel:', self.dim_kern)
        print('Zero-padded shape  :', self.dim_pad)