diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index 96be35cd527b470a163ad29208fa8776492fe23d..b51248b2b138b2128f9945faa10de663c48408f6 100644
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -5,18 +5,8 @@
<option name="ANALYSIS_IN_BACKGROUND" value="true" />
</component>
<component name="ChangeListManager">
- <list default="true" id="990252ab-aff5-4ac2-a857-b193d2c46b18" name="Default" comment="Added fieldconverter module! fieldconverter: methods to convert M to A to B magdata: a bit more parameters for quiver_plot3d(), added contour_plot3d() phasemapper: pm() extended for different projections (not just simple) kernel: u and v switched (now named after the unit magnetization direction, which makes much more sense)">
- <change type="NEW" beforePath="" afterPath="$PROJECT_DIR$/pyramid/fieldconverter.py" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/pyramid/tests/test_kernel/ref_u_fft.npy" afterPath="$PROJECT_DIR$/pyramid/tests/test_kernel/ref_u_fft.npy" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/pyramid/tests/test_kernel/ref_v_fft.npy" afterPath="$PROJECT_DIR$/pyramid/tests/test_kernel/ref_v_fft.npy" />
+ <list default="true" id="990252ab-aff5-4ac2-a857-b193d2c46b18" name="Default" comment="Refactoring: Replaced MagData with VectorData and added ScalarData class (and common superclass FieldData). magnitude is now called field (which is more appropriate) projector now uses FieldData to process both vector and scalar data (foundation was in place before)">
<change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/workspace.xml" afterPath="$PROJECT_DIR$/.idea/workspace.xml" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/pyramid/__init__.py" afterPath="$PROJECT_DIR$/pyramid/__init__.py" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/pyramid/kernel.py" afterPath="$PROJECT_DIR$/pyramid/kernel.py" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/pyramid/magdata.py" afterPath="$PROJECT_DIR$/pyramid/magdata.py" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/pyramid/phasemap.py" afterPath="$PROJECT_DIR$/pyramid/phasemap.py" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/pyramid/phasemapper.py" afterPath="$PROJECT_DIR$/pyramid/phasemapper.py" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/scripts/gui/mag_slicer.py" afterPath="$PROJECT_DIR$/scripts/gui/mag_slicer.py" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/scripts/phasemap/phasemap_tilt_series.py" afterPath="$PROJECT_DIR$/scripts/phasemap/phasemap_tilt_series.py" />
</list>
<ignored path="Pyramid.iws" />
<ignored path=".idea/workspace.xml" />
@@ -41,171 +31,11 @@
</component>
<component name="FileEditorManager">
<leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
- <file leaf-file-name="magcreator.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/pyramid/magcreator.py">
+ <file leaf-file-name="colormap.py" pinned="false" current-in-tab="true">
+ <entry file="file://$PROJECT_DIR$/pyramid/colormap.py">
<provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
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- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="projector.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/pyramid/projector.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
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- <folding />
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- </entry>
- </file>
- <file leaf-file-name="phasemapper.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/pyramid/phasemapper.py">
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- </file>
- <file leaf-file-name="test_kernel.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/pyramid/tests/test_kernel.py">
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- <folding />
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- </provider>
- </entry>
- </file>
- <file leaf-file-name="mag_slicer.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/scripts/gui/mag_slicer.py">
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- <file leaf-file-name="phasemap_creator.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/scripts/gui/phasemap_creator.py">
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- </entry>
- </file>
- <file leaf-file-name="fft.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/pyramid/fft.py">
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- <file leaf-file-name="phasemap_tilt_series.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/scripts/phasemap/phasemap_tilt_series.py">
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- <file leaf-file-name="reconstruction.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/pyramid/reconstruction.py">
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- </file>
- <file leaf-file-name="reconstruction_3d_from_magdata.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/scripts/reconstruction/reconstruction_3d_from_magdata.py">
- <provider selected="true" editor-type-id="text-editor">
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- <folding />
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- </entry>
- </file>
- <file leaf-file-name="Untitled.py" pinned="false" current-in-tab="false">
- <entry file="file://$USER_HOME$/Downloads/Untitled.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="44" column="40" selection-start-line="44" selection-start-column="40" selection-end-line="44" selection-end-column="40" />
- <folding />
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- </entry>
- </file>
- <file leaf-file-name="phasemap.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/pyramid/phasemap.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="781" column="8" selection-start-line="781" selection-start-column="8" selection-end-line="781" selection-end-column="8" />
- <folding />
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- </entry>
- </file>
- <file leaf-file-name="magdata.py" pinned="false" current-in-tab="true">
- <entry file="file://$PROJECT_DIR$/pyramid/magdata.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.62133646">
- <caret line="879" column="31" selection-start-line="879" selection-start-column="31" selection-end-line="879" selection-end-column="31" />
- <folding />
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- </provider>
- </entry>
- </file>
- <file leaf-file-name="__init__.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/pyramid/__init__.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
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- </entry>
- </file>
- <file leaf-file-name="config.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/pyramid/config.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="14" column="4" selection-start-line="14" selection-start-column="4" selection-end-line="14" selection-end-column="4" />
+ <state vertical-scroll-proportion="0.11171366">
+ <caret line="89" column="28" selection-start-line="89" selection-start-column="26" selection-end-line="89" selection-end-column="28" />
<folding />
</state>
</provider>
@@ -227,18 +57,12 @@
<component name="IdeDocumentHistory">
<option name="CHANGED_PATHS">
<list>
- <option value="$APPLICATION_CONFIG_DIR$/consoles/ide/ide-scripting.groovy" />
- <option value="$PROJECT_DIR$/../HyperSpy/.hgignore" />
- <option value="$PROJECT_DIR$/scripts/magdata/magcreator/create_array_sphere_disc_slab.py" />
<option value="$PROJECT_DIR$/../Publications/paper 2/paper2_part3_experiment.py" />
- <option value="$PROJECT_DIR$/../Publications/nanowire_z_angle.py" />
<option value="$PROJECT_DIR$/../Publications/pico 2015/poster_pico2015_2d.py" />
<option value="$PROJECT_DIR$/pyramid/numcore/__init__.py" />
<option value="$PROJECT_DIR$/../HyperSpy/hyperspy/_signals/phase_image.py" />
<option value="$PROJECT_DIR$/../HyperSpy/hyperspy/signals.py" />
<option value="$PROJECT_DIR$/pyramid/costfunction.py" />
- <option value="$PROJECT_DIR$/pyramid/projector.py" />
- <option value="$PROJECT_DIR$/pyramid/reconstruction.py" />
<option value="$PROJECT_DIR$/pyramid/regularisator.py" />
<option value="$PROJECT_DIR$/pyramid/dataset.py" />
<option value="$PROJECT_DIR$/docs/index.rst" />
@@ -249,32 +73,41 @@
<option value="$PROJECT_DIR$/pyramid/quaternion.py" />
<option value="$PROJECT_DIR$/scripts/reconstruction/reconstruction_3d_from_magdata.py" />
<option value="$PROJECT_DIR$/pyramid/forwardmodel.py" />
- <option value="$PROJECT_DIR$/pyramid/diagnostics.py" />
<option value="$PROJECT_DIR$/pyramid/fft.py" />
<option value="$PROJECT_DIR$/pyramid/version.py" />
<option value="$PROJECT_DIR$/setup.py" />
<option value="$PROJECT_DIR$/pyramid/tests/test_dataset.py" />
<option value="$PROJECT_DIR$/pyramid/tests/test_phasemap.py" />
- <option value="$PROJECT_DIR$/pyramid/tests/test_magdata.py" />
<option value="$PROJECT_DIR$/pyramid/tests/test_magcreator.py" />
<option value="$PROJECT_DIR$/pyramid/tests/test_kernel.py" />
<option value="$PROJECT_DIR$/pyramid/tests/test_forwardmodel.py" />
<option value="$PROJECT_DIR$/pyramid/tests/test_costfunction.py" />
- <option value="$PROJECT_DIR$/pyramid/tests/test_phasemapper.py" />
<option value="$PROJECT_DIR$/pyramid/tests/test_projector.py" />
<option value="$PROJECT_DIR$/pyramid/tests/test_regularisator.py" />
<option value="$PROJECT_DIR$/pyramid/tests/test_analytic.py" />
<option value="$PROJECT_DIR$/pyramid/config.py" />
<option value="$PROJECT_DIR$/pyramid/analytic.py" />
- <option value="$PROJECT_DIR$/pyramid/magcreator.py" />
<option value="$USER_HOME$/Downloads/Untitled.py" />
<option value="$PROJECT_DIR$/pyramid/__init__.py" />
- <option value="$PROJECT_DIR$/pyramid/phasemap.py" />
<option value="$PROJECT_DIR$/scripts/gui/mag_slicer.py" />
<option value="$PROJECT_DIR$/pyramid/fieldconverter.py" />
- <option value="$PROJECT_DIR$/pyramid/phasemapper.py" />
<option value="$PROJECT_DIR$/pyramid/kernel.py" />
+ <option value="$PROJECT_DIR$/pyramid/reconstruction.py" />
<option value="$PROJECT_DIR$/pyramid/magdata.py" />
+ <option value="$PROJECT_DIR$/../Publications/pico 2015/logfile.log" />
+ <option value="$PROJECT_DIR$/pyramid/phasemap.py" />
+ <option value="$PROJECT_DIR$/pyramid/diagnostics.py" />
+ <option value="$PROJECT_DIR$/pyramid/magcreator.py" />
+ <option value="$PROJECT_DIR$/pyramid/circle_interpolation.py" />
+ <option value="$PROJECT_DIR$/../Script-Vault/circle_interpolation.py" />
+ <option value="$PROJECT_DIR$/pyramid/tests/test_magdata.py" />
+ <option value="$PROJECT_DIR$/pyramid/tests/test_fielddata.py" />
+ <option value="$PROJECT_DIR$/../Publications/nanowire_z_angle.py" />
+ <option value="$PROJECT_DIR$/pyramid/projector.py" />
+ <option value="$PROJECT_DIR$/pyramid/fielddata.py" />
+ <option value="$PROJECT_DIR$/pyramid/tests/test_phasemapper.py" />
+ <option value="$PROJECT_DIR$/pyramid/phasemapper.py" />
+ <option value="$PROJECT_DIR$/scripts/phasemap/phasemap_tilt_series.py" />
</list>
</option>
</component>
@@ -340,34 +173,8 @@
<foldersAlwaysOnTop value="true" />
</navigator>
<panes>
- <pane id="Scope">
- <subPane subId="Changed Files">
- <PATH>
- <PATH_ELEMENT USER_OBJECT="Root">
- <option name="myItemId" value="" />
- <option name="myItemType" value="" />
- </PATH_ELEMENT>
- <PATH_ELEMENT USER_OBJECT="Pyramid">
- <option name="myItemId" value="" />
- <option name="myItemType" value="" />
- </PATH_ELEMENT>
- </PATH>
- <PATH>
- <PATH_ELEMENT USER_OBJECT="Root">
- <option name="myItemId" value="" />
- <option name="myItemType" value="" />
- </PATH_ELEMENT>
- <PATH_ELEMENT USER_OBJECT="Pyramid">
- <option name="myItemId" value="" />
- <option name="myItemType" value="" />
- </PATH_ELEMENT>
- <PATH_ELEMENT USER_OBJECT="pyramid">
- <option name="myItemId" value="" />
- <option name="myItemType" value="" />
- </PATH_ELEMENT>
- </PATH>
- </subPane>
- </pane>
+ <pane id="Scope" />
+ <pane id="Scratches" />
<pane id="ProjectPane">
<subPane>
<PATH>
@@ -386,56 +193,6 @@
<option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
</PATH_ELEMENT>
</PATH>
- <PATH>
- <PATH_ELEMENT>
- <option name="myItemId" value="Pyramid" />
- <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
- </PATH_ELEMENT>
- <PATH_ELEMENT>
- <option name="myItemId" value="Pyramid" />
- <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
- </PATH_ELEMENT>
- <PATH_ELEMENT>
- <option name="myItemId" value="scripts" />
- <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
- </PATH_ELEMENT>
- <PATH_ELEMENT>
- <option name="myItemId" value="reconstruction" />
- <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
- </PATH_ELEMENT>
- </PATH>
- <PATH>
- <PATH_ELEMENT>
- <option name="myItemId" value="Pyramid" />
- <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
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- <PATH_ELEMENT>
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- <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
- </PATH_ELEMENT>
- <PATH_ELEMENT>
- <option name="myItemId" value="scripts" />
- <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
- </PATH_ELEMENT>
- </PATH>
- <PATH>
- <PATH_ELEMENT>
- <option name="myItemId" value="Pyramid" />
- <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
- </PATH_ELEMENT>
- <PATH_ELEMENT>
- <option name="myItemId" value="Pyramid" />
- <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
- </PATH_ELEMENT>
- <PATH_ELEMENT>
- <option name="myItemId" value="scripts" />
- <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
- </PATH_ELEMENT>
- <PATH_ELEMENT>
- <option name="myItemId" value="gui" />
- <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
- </PATH_ELEMENT>
- </PATH>
<PATH>
<PATH_ELEMENT>
<option name="myItemId" value="Pyramid" />
@@ -452,7 +209,6 @@
</PATH>
</subPane>
</pane>
- <pane id="Scratches" />
<pane id="ColorIdeProjectViewPane">
<subPane>
<PATH>
@@ -476,9 +232,9 @@
</panes>
</component>
<component name="PropertiesComponent">
- <property name="settings.editor.selected.configurable" value="reference.settingsdialog.IDE.editor.colors.Debugger" />
+ <property name="settings.editor.selected.configurable" value="editor.preferences.tabs" />
<property name="settings.editor.splitter.proportion" value="0.2" />
- <property name="last_opened_file_path" value="$PROJECT_DIR$/docs/_build" />
+ <property name="last_opened_file_path" value="$PROJECT_DIR$/files/vecdata" />
<property name="FileHistory.org.zmlx.hg4idea.provider.HgHistoryProvider_flatWidth0" value="44" />
<property name="FileHistory.org.zmlx.hg4idea.provider.HgHistoryProvider_flatOrder0" value="0" />
<property name="FileHistory.org.zmlx.hg4idea.provider.HgHistoryProvider_flatWidth1" value="64" />
@@ -497,6 +253,7 @@
<property name="FileHistory.org.zmlx.hg4idea.provider.HgHistoryProvider_treeOrder3" value="3" />
<property name="last.edited.regexp" value="asdf aasfasf.version_info " />
<property name="restartRequiresConfirmation" value="false" />
+ <property name="SearchEverywhereHistoryKey" value="colorwheel	null	null" />
</component>
<component name="Push.Settings">
<excluded-roots>
@@ -505,11 +262,11 @@
</component>
<component name="PyConsoleOptionsProvider">
<option name="myPythonConsoleState">
- <console-settings custom-start-script="# coding: utf-8 """Startup!""" from __future__ import division import sys import os import pdb import hyperspy.api as hs import pyramid from pyramid import * import pyramid.analytic as an import pyramid.magcreator as mc import pyramid.reconstruction as rc import jutil import numpy as np import scipy as sp import matplotlib as mpl import matplotlib.pyplot as plt from pylab import * import logging.config logging.config.fileConfig(LOGGING_CONFIG, disable_existing_loggers=False) ion() # Enable Matplotlib's interactive mode sys.path.extend([WORKING_DIR_AND_PYTHON_PATHS]) " module-name="Pyramid" is-module-sdk="true" working-directory="$PROJECT_DIR$/files/magdata">
+ <console-settings custom-start-script="# coding: utf-8 """Startup!""" from __future__ import division import sys import os import pdb import hyperspy.api as hs import pyramid from pyramid import * import pyramid.analytic as an import pyramid.magcreator as mc import pyramid.reconstruction as rc import jutil import numpy as np import scipy as sp import matplotlib as mpl import matplotlib.pyplot as plt from pylab import * import logging.config logging.config.fileConfig(LOGGING_CONFIG, disable_existing_loggers=False) ion() # Enable Matplotlib's interactive mode sys.path.extend([WORKING_DIR_AND_PYTHON_PATHS]) " module-name="Pyramid" is-module-sdk="true" working-directory="$PROJECT_DIR$/files/vecdata">
<option name="myCustomStartScript" value="# coding: utf-8 """Startup!""" from __future__ import division import sys import os import pdb import hyperspy.api as hs import pyramid from pyramid import * import pyramid.analytic as an import pyramid.magcreator as mc import pyramid.reconstruction as rc import jutil import numpy as np import scipy as sp import matplotlib as mpl import matplotlib.pyplot as plt from pylab import * import logging.config logging.config.fileConfig(LOGGING_CONFIG, disable_existing_loggers=False) ion() # Enable Matplotlib's interactive mode sys.path.extend([WORKING_DIR_AND_PYTHON_PATHS]) " />
<option name="myUseModuleSdk" value="true" />
<option name="myModuleName" value="Pyramid" />
- <option name="myWorkingDirectory" value="$PROJECT_DIR$/files/magdata" />
+ <option name="myWorkingDirectory" value="$PROJECT_DIR$/files/vecdata" />
<option name="myAddSourceRoots" value="true" />
</console-settings>
</option>
@@ -535,45 +292,87 @@
<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<module name="Pyramid" />
- <option name="SCRIPT_NAME" value="$PROJECT_DIR$/pyramid/magdata.py" />
+ <option name="SCRIPT_NAME" value="C:\Users\Jan\Home\PhD Thesis\Projects\Pyramid\pyramid\fielddata.py" />
<option name="PARAMETERS" value="" />
<option name="SHOW_COMMAND_LINE" value="true" />
<method />
</configuration>
- <configuration default="false" name="setup" type="PythonConfigurationType" factoryName="Python" temporary="true">
+ <configuration default="false" name="circle_interpolation" type="PythonConfigurationType" factoryName="Python" singleton="true" temporary="true">
<option name="INTERPRETER_OPTIONS" value="" />
<option name="PARENT_ENVS" value="true" />
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+ <caret line="30" column="0" selection-start-line="30" selection-start-column="0" selection-end-line="30" selection-end-column="0" />
<folding />
</state>
</provider>
</entry>
- <entry file="file://$PROJECT_DIR$/pyramid/phasemapper.py">
+ <entry file="file://$PROJECT_DIR$/../Publications/tilt_series.py">
<provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="-8.666667">
- <caret line="332" column="51" selection-start-line="332" selection-start-column="51" selection-end-line="332" selection-end-column="51" />
+ <state vertical-scroll-proportion="0.6496746">
+ <caret line="38" column="36" selection-start-line="38" selection-start-column="36" selection-end-line="38" selection-end-column="36" />
<folding />
</state>
</provider>
</entry>
- <entry file="file://$PROJECT_DIR$/pyramid/kernel.py">
+ <entry file="file://$PROJECT_DIR$/pyramid/fielddata.py">
<provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="95" column="34" selection-start-line="95" selection-start-column="34" selection-end-line="95" selection-end-column="34" />
+ <state vertical-scroll-proportion="0.55748373">
+ <caret line="330" column="58" selection-start-line="330" selection-start-column="58" selection-end-line="330" selection-end-column="58" />
<folding />
</state>
</provider>
</entry>
- <entry file="file://$PROJECT_DIR$/scripts/phasemap/phasemap_tilt_series.py">
+ <entry file="file://$PROJECT_DIR$/pyramid/__init__.py">
<provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="40" column="16" selection-start-line="40" selection-start-column="16" selection-end-line="40" selection-end-column="16" />
+ <state vertical-scroll-proportion="0.52060735">
+ <caret line="90" column="38" selection-start-line="90" selection-start-column="38" selection-end-line="90" selection-end-column="38" />
<folding />
</state>
</provider>
</entry>
- <entry file="file://$PROJECT_DIR$/pyramid/magdata.py">
+ <entry file="file://$PROJECT_DIR$/pyramid/colormap.py">
<provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.62133646">
- <caret line="879" column="31" selection-start-line="879" selection-start-column="31" selection-end-line="879" selection-end-column="31" />
+ <state vertical-scroll-proportion="0.11171366">
+ <caret line="89" column="28" selection-start-line="89" selection-start-column="26" selection-end-line="89" selection-end-column="28" />
<folding />
</state>
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diff --git a/pyramid/__init__.py b/pyramid/__init__.py
index d45cdbbec436ce7f14eabc7702f2e312e27905dd..2c8ec1d833c00d80b73f31da9f7337fb0f7e4e0e 100644
--- a/pyramid/__init__.py
+++ b/pyramid/__init__.py
@@ -70,8 +70,8 @@ from . import forwardmodel
from .forwardmodel import *
from . import kernel
from .kernel import *
-from . import magdata
-from .magdata import *
+from . import fielddata
+from .fielddata import *
from . import phasemap
from .phasemap import *
from . import phasemapper
@@ -99,7 +99,7 @@ __all__.extend(dataset.__all__)
__all__.extend(diagnostics.__all__)
__all__.extend(forwardmodel.__all__)
__all__.extend(kernel.__all__)
-__all__.extend(magdata.__all__)
+__all__.extend(fielddata.__all__)
__all__.extend(phasemap.__all__)
__all__.extend(phasemapper.__all__)
__all__.extend(projector.__all__)
diff --git a/pyramid/dataset.py b/pyramid/dataset.py
index c32c73e802ffa5e4cf9a504d8266631bdd8213f4..34501da6d74fade3115976148303a0c68c628f7a 100644
--- a/pyramid/dataset.py
+++ b/pyramid/dataset.py
@@ -157,11 +157,11 @@ class DataSet(object):
def create_phase_maps(self, mag_data):
"""Create a list of phasemaps with the projectors in the dataset for a given
- :class:`~.MagData` object.
+ :class:`~.VectorData` object.
Parameters
----------
- mag_data : :class:`~.MagData`
+ mag_data : :class:`~.VectorData`
Magnetic distribution to which the projectors of the dataset should be applied.
Returns
@@ -280,7 +280,7 @@ class DataSet(object):
Parameters
----------
- mag_data : :class:`~.MagData`, optional
+ mag_data : :class:`~.VectorData`, optional
Magnetic distribution to which the projectors of the dataset should be applied. If not
given, the phase_maps in the dataset are used.
title : string, optional
@@ -317,7 +317,7 @@ class DataSet(object):
Parameters
----------
- mag_data : :class:`~.MagData`, optional
+ mag_data : :class:`~.VectorData`, optional
Magnetic distribution to which the projectors of the dataset should be applied. If not
given, the phase_maps in the dataset are used.
title : string, optional
diff --git a/pyramid/diagnostics.py b/pyramid/diagnostics.py
index 74274d0b0ee6b0b10d467cf320c13abdd1b90ffe..eb0bb7a10916b94d65acf385a35143ff4014c57e 100644
--- a/pyramid/diagnostics.py
+++ b/pyramid/diagnostics.py
@@ -12,7 +12,7 @@ import numpy as np
import jutil
from pyramid import fft
-from pyramid.magdata import MagData
+from pyramid.fielddata import VectorData
from pyramid.phasemap import PhaseMap
__all__ = ['Diagnostics']
@@ -157,14 +157,14 @@ class Diagnostics(object):
Returns
-------
- mag_data_avg_kern: :class:`~pyramid.magdata.MagData`
+ mag_data_avg_kern: :class:`~pyramid.fielddata.VectorData`
Averaging kernel matrix row represented as a 3D magnetization distribution
"""
self._log.debug('Calling get_avg_kern_row')
if pos is not None:
self.pos = pos
- mag_data_avg_kern = MagData(self.cost.data_set.a, fft.zeros((3,) + self.dim))
+ mag_data_avg_kern = VectorData(self.cost.data_set.a, fft.zeros((3,) + self.dim))
mag_data_avg_kern.set_vector(self.avrg_kern_row, mask=self.mask)
return mag_data_avg_kern
@@ -181,7 +181,7 @@ class Diagnostics(object):
px_avrg: float
The number of pixels over which is approximately averaged. The inverse is the FWHM.
(x, y, z): tuple of floats
- The magnitude of the averaging kernel summed along two axes (the remaining are x, y, z,
+ The field of the averaging kernel summed along two axes (the remaining are x, y, z,
respectively).
Notes
@@ -191,7 +191,7 @@ class Diagnostics(object):
"""
self._log.debug('Calling calculate_averaging')
mag_data_avg_kern = self.get_avg_kern_row(pos)
- mag_x, mag_y, mag_z = mag_data_avg_kern.magnitude
+ mag_x, mag_y, mag_z = mag_data_avg_kern.field
x = mag_x.sum(axis=(0, 1))
y = mag_y.sum(axis=(0, 2))
z = mag_z.sum(axis=(1, 2))
diff --git a/pyramid/fieldconverter.py b/pyramid/fieldconverter.py
index 0b5e29fbb9643d335651b220068ac50818844e1a..a40413ee1338ccfba71bd357f48cdbdbaa3daa50 100644
--- a/pyramid/fieldconverter.py
+++ b/pyramid/fieldconverter.py
@@ -12,7 +12,7 @@ import logging
import numpy as np
from pyramid import fft
-from pyramid.magdata import MagData
+from pyramid.fielddata import VectorData
__all__ = ['convert_M_to_A', 'convert_A_to_B', 'convert_M_to_B']
_log = logging.getLogger(__name__)
@@ -23,20 +23,20 @@ def convert_M_to_A(mag_data, b_0=1.0):
Parameters
----------
- mag_data: :class:`~pyramid.magdata.MagData` object
+ mag_data: :class:`~pyramid.magdata.VectorData` object
The magnetic vector field from which the A-field is calculated.
b_0: float, optional
The saturation magnetization which is used in the calculation.
Returns
-------
- b_data: :class:`~pyramid.magdata.MagData` object
+ b_data: :class:`~pyramid.magdata.VectorData` object
The calculated B-field.
"""
_log.debug('Calling convert_M_to_A')
# Preparations of variables:
- assert isinstance(mag_data, MagData), 'Only MagData objects can be mapped!'
+ assert isinstance(mag_data, VectorData), 'Only VectorData objects can be mapped!'
dim = mag_data.dim
dim_kern = tuple(2 * np.array(dim) - 1) # Dimensions of the kernel
if fft.BACKEND == 'pyfftw':
@@ -71,9 +71,9 @@ def convert_M_to_A(mag_data, b_0=1.0):
x_mag = fft.zeros(dim_pad, dtype=fft.FLOAT)
y_mag = fft.zeros(dim_pad, dtype=fft.FLOAT)
z_mag = fft.zeros(dim_pad, dtype=fft.FLOAT)
- x_mag[slice_M] = mag_data.magnitude[0, ...]
- y_mag[slice_M] = mag_data.magnitude[1, ...]
- z_mag[slice_M] = mag_data.magnitude[2, ...]
+ x_mag[slice_M] = mag_data.field[0, ...]
+ y_mag[slice_M] = mag_data.field[1, ...]
+ z_mag[slice_M] = mag_data.field[2, ...]
# Calculate Fourier trafo of magnetization components:
x_mag_fft = fft.rfftn(x_mag)
y_mag_fft = fft.rfftn(y_mag)
@@ -86,7 +86,7 @@ def convert_M_to_A(mag_data, b_0=1.0):
a_y = fft.irfftn(a_y_fft)[slice_B]
a_z = fft.irfftn(a_z_fft)[slice_B]
# Return A-field:
- return MagData(mag_data.a, np.asarray((a_x, a_y, a_z)))
+ return VectorData(mag_data.a, np.asarray((a_x, a_y, a_z)))
def convert_A_to_B(a_data):
@@ -94,19 +94,19 @@ def convert_A_to_B(a_data):
Parameters
----------
- a_data: :class:`~pyramid.magdata.MagData` object
+ a_data: :class:`~pyramid.magdata.VectorData` object
The vector potential field from which the A-field is calculated.
Returns
-------
- b_data: :class:`~pyramid.magdata.MagData` object
+ b_data: :class:`~pyramid.magdata.VectorData` object
The calculated B-field.
"""
_log.debug('Calling convert_A_to_B')
- assert isinstance(a_data, MagData), 'Only MagData objects can be mapped!'
+ assert isinstance(a_data, VectorData), 'Only VectorData objects can be mapped!'
# Calculate gradients:
- x_mag, y_mag, z_mag = a_data.magnitude
+ x_mag, y_mag, z_mag = a_data.field
x_grad_z, x_grad_y, x_grad_x = np.gradient(x_mag)
y_grad_z, y_grad_y, y_grad_x = np.gradient(y_mag)
z_grad_z, z_grad_y, z_grad_x = np.gradient(z_mag)
@@ -115,7 +115,7 @@ def convert_A_to_B(a_data):
b_y = (x_grad_z - z_grad_x)
b_z = (y_grad_x - x_grad_y)
# Return B-field:
- return MagData(a_data.a, np.asarray((b_x, b_y, b_z)))
+ return VectorData(a_data.a, np.asarray((b_x, b_y, b_z)))
def convert_M_to_B(mag_data, b_0=1.0):
@@ -123,17 +123,17 @@ def convert_M_to_B(mag_data, b_0=1.0):
Parameters
----------
- mag_data: :class:`~pyramid.magdata.MagData` object
+ mag_data: :class:`~pyramid.magdata.VectorData` object
The magnetic vector field from which the B-field is calculated.
b_0: float, optional
The saturation magnetization which is used in the calculation.
Returns
-------
- b_data: :class:`~pyramid.magdata.MagData` object
+ b_data: :class:`~pyramid.magdata.VectorData` object
The calculated B-field.
"""
_log.debug('Calling convert_M_to_B')
- assert isinstance(mag_data, MagData), 'Only MagData objects can be mapped!'
+ assert isinstance(mag_data, VectorData), 'Only VectorData objects can be mapped!'
return convert_A_to_B(convert_M_to_A(mag_data, b_0=b_0))
diff --git a/pyramid/magdata.py b/pyramid/fielddata.py
similarity index 50%
rename from pyramid/magdata.py
rename to pyramid/fielddata.py
index e740e2b120d822b5cb3abf66dafa7c78b4e45ef0..4301d1f785d744c8ff7a571a333e80e7912d5a1a 100644
--- a/pyramid/magdata.py
+++ b/pyramid/fielddata.py
@@ -2,16 +2,17 @@
# Copyright 2014 by Forschungszentrum Juelich GmbH
# Author: J. Caron
#
-"""This module provides the :class:`~.MagData` class for storing of magnetization data."""
+"""This module provides classes for storing vector and scalar 3D-field."""
from __future__ import division
import logging
import os
+from abc import ABCMeta, abstractmethod
from numbers import Number
-import matplotlib.pyplot as plt
import numpy as np
+from matplotlib import pyplot as plt
from matplotlib.ticker import MaxNLocator
from scipy.ndimage.interpolation import zoom
@@ -25,31 +26,31 @@ except ImportError:
hs = None
_log.error('Could not load hyperspy package!')
-__all__ = ['MagData']
+__all__ = ['VectorData', 'ScalarData']
-class MagData(object):
- """Class for storing magnetization data.
+class FieldData(object):
+ """Class for storing field data.
- Represents 3-dimensional magnetic distributions with 3 components which are stored as a
- 2-dimensional numpy array in `magnitude`, but which can also be accessed as a vector via
- `mag_vec`. :class:`~.MagData` objects support negation, arithmetic operators
+ Abstract base class for the representatio of magnetic or electric fields (see subclasses).
+ Fields can be accessed as 3D numpy arrays via the `field` property or as a vector via
+ `field_vec`. :class:`~.FieldData` objects support negation, arithmetic operators
(``+``, ``-``, ``*``) and their augmented counterparts (``+=``, ``-=``, ``*=``), with numbers
- and other :class:`~.MagData` objects, if their dimensions and grid spacings match. It is
- possible to load data from HDF5 or LLG (.txt) files or to save the data in these formats.
- Plotting methods are also provided.
+ and other :class:`~.FieldData` objects of the same subclass, if their dimensions and grid
+ spacings match. It is possible to load data from HDF5 or LLG (.txt) files or to save the data
+ in these formats. Specialised plotting methods are also provided.
Attributes
----------
a: float
The grid spacing in nm.
- magnitude: :class:`~numpy.ndarray` (N=4)
- The `x`-, `y`- and `z`-component of the magnetization vector for every 3D-gridpoint
- as a 4-dimensional numpy array (first dimension has to be 3, because of the 3 components).
+ field: :class:`~numpy.ndarray` (N=4)
+ The field distribution for every 3D-gridpoint.
"""
- _log = logging.getLogger(__name__ + '.MagData')
+ __metaclass__ = ABCMeta
+ _log = logging.getLogger(__name__ + '.FieldData')
@property
def a(self):
@@ -62,73 +63,80 @@ class MagData(object):
assert a >= 0, 'Grid spacing has to be a positive number!'
self._a = float(a)
+ @property
+ def shape(self):
+ """The shape of the `field` (3D for scalar, 4D vor vector field)."""
+ return self.field.shape
+
@property
def dim(self):
- """Dimensions (z, y, x) of the grid."""
- return self._dim
+ """Dimensions (z, y, x) of the grid, only 3D coordinates, without components if present."""
+ return self.shape[-3:]
@property
- def magnitude(self):
- """The `x`-, `y`- and `z`-component of the magnetization vector for every 3D-gridpoint."""
- return self._magnitude
-
- @magnitude.setter
- def magnitude(self, magnitude):
- assert isinstance(magnitude, np.ndarray), 'Magnitude has to be a numpy array!'
- assert len(magnitude.shape) == 4, 'Magnitude has to be 4-dimensional!'
- assert magnitude.shape[0] == 3, 'First dimension of the magnitude has to be 3!'
- self._magnitude = np.asarray(magnitude, dtype=fft.FLOAT)
- self._dim = magnitude.shape[1:]
+ def field(self):
+ """The field strength for every 3D-gridpoint (scalar: 3D, vector: 4D)."""
+ return self._field
+
+ @field.setter
+ def field(self, field):
+ assert isinstance(field, np.ndarray), 'Field has to be a numpy array!'
+ assert 3 <= len(field.shape) <= 4, 'Field has to be 3- or 4-dimensional (scalar / vector)!'
+ if len(field.shape) == 4:
+ assert field.shape[0] == 3, 'A vector field has to have exactly 3 components!'
+ self._field = np.asarray(field, dtype=fft.FLOAT)
@property
- def mag_amp(self):
- """The length (amplitude) of the magnetization vectors as a 3D-array."""
- return np.sqrt(np.sum(self.magnitude ** 2, axis=0))
+ def field_amp(self):
+ """The field amplitude (returns the field itself for scalar and the vector amplitude
+ calculated via a square sum for a vector field."""
+ if len(self.shape) == 4:
+ return np.sqrt(np.sum(self.field ** 2, axis=0))
+ else:
+ return self.field
@property
- def mag_vec(self):
- """Vector containing the magnetic distribution."""
- return np.reshape(self.magnitude, -1)
+ def field_vec(self):
+ """Vector containing the vector field distribution."""
+ return np.reshape(self.field, -1)
- @mag_vec.setter
- def mag_vec(self, mag_vec):
+ @field_vec.setter
+ def field_vec(self, mag_vec):
mag_vec = np.asarray(mag_vec, dtype=fft.FLOAT)
- assert np.size(mag_vec) == 3 * np.prod(self.dim), \
- 'Vector has to match magnitude dimensions! {} {}'.format(mag_vec.shape,
- 3 * np.prod(self.dim))
- self.magnitude = mag_vec.reshape((3,) + self.dim)
+ assert np.size(mag_vec) == np.prod(self.shape), \
+ 'Vector has to match field shape! {} {}'.format(mag_vec.shape, np.prod(self.shape))
+ self.field = mag_vec.reshape((3,) + self.dim)
- def __init__(self, a, magnitude):
+ def __init__(self, a, field):
self._log.debug('Calling __init__')
self.a = a
- self.magnitude = magnitude
+ self.field = field
self._log.debug('Created ' + str(self))
def __repr__(self):
self._log.debug('Calling __repr__')
- return '%s(a=%r, magnitude=%r)' % (self.__class__, self.a, self.magnitude)
+ return '%s(a=%r, field=%r)' % (self.__class__, self.a, self.field)
def __str__(self):
self._log.debug('Calling __str__')
- return 'MagData(a=%s, dim=%s)' % (self.a, self.dim)
+ return '%s(a=%s, dim=%s)' % (self.__class__, self.a, self.dim)
def __neg__(self): # -self
self._log.debug('Calling __neg__')
- return MagData(self.a, -self.magnitude)
+ return VectorData(self.a, -self.field)
def __add__(self, other): # self + other
self._log.debug('Calling __add__')
- assert isinstance(other, (MagData, Number)), \
- 'Only MagData objects and scalar numbers (as offsets) can be added/subtracted!'
- if isinstance(other, MagData):
- self._log.debug('Adding two MagData objects')
+ assert isinstance(other, (FieldData, Number)), \
+ 'Only FieldData objects and scalar numbers (as offsets) can be added/subtracted!'
+ if isinstance(other, FieldData):
+ self._log.debug('Adding two VectorData objects')
assert other.a == self.a, 'Added phase has to have the same grid spacing!'
- assert other.magnitude.shape == (3,) + self.dim, \
- 'Added magnitude has to have the same dimensions!'
- return MagData(self.a, self.magnitude + other.magnitude)
+ assert other.shape == self.shape, 'Added field has to have the same dimensions!'
+ return self.__init__(self.a, self.field + other.field)
else: # other is a Number
self._log.debug('Adding an offset')
- return MagData(self.a, self.magnitude + other)
+ return self.__init__(self.a, self.field + other)
def __sub__(self, other): # self - other
self._log.debug('Calling __sub__')
@@ -136,8 +144,8 @@ class MagData(object):
def __mul__(self, other): # self * other
self._log.debug('Calling __mul__')
- assert isinstance(other, Number), 'MagData objects can only be multiplied by numbers!'
- return MagData(self.a, other * self.magnitude)
+ assert isinstance(other, Number), 'FieldData objects can only be multiplied by numbers!'
+ return VectorData(self.a, other * self.field)
def __radd__(self, other): # other + self
self._log.debug('Calling __radd__')
@@ -164,24 +172,211 @@ class MagData(object):
return self.__mul__(other)
def copy(self):
- """Returns a copy of the :class:`~.MagData` object
+ """Returns a copy of the :class:`~.FieldData` object
Returns
-------
- mag_data: :class:`~.MagData`
- A copy of the :class:`~.MagData`.
+ field_data: :class:`~.FieldData`
+ A copy of the :class:`~.FieldData`.
"""
self._log.debug('Calling copy')
- return MagData(self.a, self.magnitude.copy())
+ return self.__init__(self.a, self.field.copy())
+
+ def get_mask(self, threshold=0):
+ """Mask all pixels where the amplitude of the field lies above `threshold`.
+
+ Parameters
+ ----------
+ threshold : float, optional
+ A pixel only gets masked, if it lies above this threshold . The default is 0.
+
+ Returns
+ -------
+ mask : :class:`~numpy.ndarray` (N=3, boolean)
+ Mask of the pixels where the amplitude of the field lies above `threshold`.
+
+ """
+ self._log.debug('Calling get_mask')
+ return np.where(self.field_amp > threshold, True, False)
+
+ def contour_plot3d(self, title='Field Distribution', contours=10, opacity=0.25):
+ """Plot the field as a 3D-contour plot.
+
+ Parameters
+ ----------
+ title: string, optional
+ The title for the plot.
+ contours: int, optional
+ Number of contours which should be plotted.
+ opacity: float, optional
+ Defines the opacity of the contours. Default is 0.25.
+
+ Returns
+ -------
+ plot : :class:`mayavi.modules.vectors.Vectors`
+ The plot object.
+
+
+ """
+ self._log.debug('Calling quiver_plot3D')
+ from mayavi import mlab
+ # Plot them as vectors:
+ mlab.figure(size=(750, 700))
+ plot = mlab.contour3d(self.field_amp, contours=contours, opacity=opacity)
+ mlab.outline(plot)
+ mlab.axes(plot)
+ mlab.title(title, height=0.95, size=0.35)
+ mlab.orientation_axes()
+ # mlab.show()
+ return plot
+
+ @abstractmethod
+ def scale_down(self, n):
+ """Scale down the field distribution by averaging over two pixels along each axis.
+
+ Parameters
+ ----------
+ n : int, optional
+ Number of times the field distribution is scaled down. The default is 1.
+
+ Returns
+ -------
+ None
+
+ Notes
+ -----
+ Acts in place and changes dimensions and grid spacing accordingly.
+ Only possible, if each axis length is a power of 2!
+
+ """
+ pass
+
+ @abstractmethod
+ def scale_up(self, n, order):
+ """Scale up the field distribution using spline interpolation of the requested order.
+
+ Parameters
+ ----------
+ n : int, optional
+ Power of 2 with which the grid is scaled. Default is 1, which means every axis is
+ increased by a factor of ``2**1 = 2``.
+ order : int, optional
+ The order of the spline interpolation, which has to be in the range between 0 and 5
+ and defaults to 0.
+
+ Returns
+ -------
+ None
+
+ Notes
+ -----
+ Acts in place and changes dimensions and grid spacing accordingly.
+ """
+ pass
+
+ @abstractmethod
+ def get_vector(self, mask):
+ """Returns the field as a vector, specified by a mask.
+
+ Parameters
+ ----------
+ mask : :class:`~numpy.ndarray` (N=3, boolean)
+ Masks the pixels from which the entries should be taken.
+
+ Returns
+ -------
+ vector : :class:`~numpy.ndarray` (N=1)
+ The vector containing the field of the specified pixels.
+
+ """
+ pass
+
+ @abstractmethod
+ def set_vector(self, vector, mask):
+ """Set the field of the masked pixels to the values specified by `vector`.
+
+ Parameters
+ ----------
+ mask : :class:`~numpy.ndarray` (N=3, boolean), optional
+ Masks the pixels from which the field should be taken.
+ vector : :class:`~numpy.ndarray` (N=1)
+ The vector containing the field of the specified pixels.
+
+ Returns
+ -------
+ None
+
+ """
+ pass
+
+ @abstractmethod
+ def to_signal(self):
+ """Convert :class:`~.FieldData` data into a HyperSpy signal.
+
+ Returns
+ -------
+ signal: :class:`~hyperspy.signals.Signal`
+ Representation of the :class:`~.FieldData` object as a HyperSpy Signal.
+
+ Notes
+ -----
+ This method recquires the hyperspy package!
+
+ """
+ pass
+
+ @abstractmethod
+ def save_to_hdf5(self, filename):
+ """Save field data in a file with HyperSpys HDF5-format.
+
+ Parameters
+ ----------
+ filename : string, optional
+ The name of the HDF5-file in which to store the field data.
+
+ Returns
+ -------
+ None
+
+ """
+ pass
+
+
+class VectorData(FieldData):
+ """Class for storing vector ield data.
+
+ Represents 3-dimensional vector field distributions with 3 components which are stored as a
+ 3-dimensional numpy array in `field`, but which can also be accessed as a vector via
+ `field_vec`. :class:`~.VectorData` objects support negation, arithmetic operators
+ (``+``, ``-``, ``*``) and their augmented counterparts (``+=``, ``-=``, ``*=``), with numbers
+ and other :class:`~.VectorData` objects, if their dimensions and grid spacings match. It is
+ possible to load data from HDF5 or LLG (.txt) files or to save the data in these formats.
+ Plotting methods are also provided.
+
+ Attributes
+ ----------
+ a: float
+ The grid spacing in nm.
+ field: :class:`~numpy.ndarray` (N=4)
+ The `x`-, `y`- and `z`-component of the vector field for every 3D-gridpoint
+ as a 4-dimensional numpy array (first dimension has to be 3, because of the 3 components).
+
+ """
+ _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 magnetic distribution by averaging over two pixels along each axis.
+ """Scale down the field distribution by averaging over two pixels along each axis.
Parameters
----------
n : int, optional
- Number of times the magnetic distribution is scaled down. The default is 1.
+ Number of times the field distribution is scaled down. The default is 1.
Returns
-------
@@ -200,14 +395,14 @@ class MagData(object):
# Pad if necessary:
pz, py, px = self.dim[0] % 2, self.dim[1] % 2, self.dim[2] % 2
if pz != 0 or py != 0 or px != 0:
- self.magnitude = np.pad(self.magnitude, ((0, 0), (0, pz), (0, py), (0, px)),
- mode='constant')
- # Create coarser grid for the magnetization:
+ self.field = np.pad(self.field, ((0, 0), (0, pz), (0, py), (0, px)),
+ mode='constant')
+ # Create coarser grid for the vector field:
shape_4d = (3, self.dim[0] / 2, 2, self.dim[1] / 2, 2, self.dim[2] / 2, 2)
- self.magnitude = self.magnitude.reshape(shape_4d).mean(axis=(6, 4, 2))
+ self.field = self.field.reshape(shape_4d).mean(axis=(6, 4, 2))
def scale_up(self, n=1, order=0):
- """Scale up the magnetic distribution using spline interpolation of the requested order.
+ """Scale up the field distribution using spline interpolation of the requested order.
Parameters
----------
@@ -231,12 +426,12 @@ class MagData(object):
assert 5 > order >= 0 and isinstance(order, (int, long)), \
'order must be a positive integer between 0 and 5!'
self.a /= 2 ** n
- self.magnitude = np.array((zoom(self.magnitude[0], zoom=2 ** n, order=order),
- zoom(self.magnitude[1], zoom=2 ** n, order=order),
- zoom(self.magnitude[2], zoom=2 ** n, order=order)))
+ self.field = np.array((zoom(self.field[0], zoom=2 ** n, order=order),
+ zoom(self.field[1], zoom=2 ** n, order=order),
+ zoom(self.field[2], zoom=2 ** n, order=order)))
def pad(self, pad_values):
- """Pad the current magnetic distribution with zeros for each individual axis.
+ """Pad the current field distribution with zeros for each individual axis.
Parameters
----------
@@ -259,12 +454,12 @@ class MagData(object):
for i, values in enumerate(pad_values):
assert np.shape(values) in [(), (2,)], 'Only one or two values per axis can be given!'
pv[2 * i:2 * (i + 1)] = values
- self.magnitude = np.pad(self.magnitude,
- ((0, 0), (pv[0], pv[1]), (pv[2], pv[3]), (pv[4], pv[5])),
- mode='constant')
+ self.field = np.pad(self.field,
+ ((0, 0), (pv[0], pv[1]), (pv[2], pv[3]), (pv[4], pv[5])),
+ mode='constant')
def crop(self, crop_values):
- """Crop the current magnetic distribution with zeros for each individual axis.
+ """Crop the current field distribution with zeros for each individual axis.
Parameters
----------
@@ -289,27 +484,10 @@ class MagData(object):
cv[2 * i:2 * (i + 1)] = values
cv *= np.resize([1, -1], len(cv))
cv = np.where(cv == 0, None, cv)
- self.magnitude = self.magnitude[:, cv[0]:cv[1], cv[2]:cv[3], cv[4]:cv[5]]
-
- def get_mask(self, threshold=0):
- """Mask all pixels where the amplitude of the magnetization lies above `threshold`.
-
- Parameters
- ----------
- threshold : float, optional
- A pixel only gets masked, if it lies above this threshold . The default is 0.
-
- Returns
- -------
- mask : :class:`~numpy.ndarray` (N=3, boolean)
- Mask of the pixels where the amplitude of the magnetization lies above `threshold`.
-
- """
- self._log.debug('Calling get_mask')
- return np.where(self.mag_amp > threshold, True, False)
+ self.field = self.field[:, cv[0]:cv[1], cv[2]:cv[3], cv[4]:cv[5]]
def get_vector(self, mask):
- """Returns the magnetic components arranged in a vector, specified by a mask.
+ """Returns the vector field components arranged in a vector, specified by a mask.
Parameters
----------
@@ -319,27 +497,27 @@ class MagData(object):
Returns
-------
vector : :class:`~numpy.ndarray` (N=1)
- The vector containing magnetization components of the specified pixels.
+ The vector containing vector field components of the specified pixels.
Order is: first all `x`-, then all `y`-, then all `z`-components.
"""
self._log.debug('Calling get_vector')
if mask is not None:
- return np.reshape([self.magnitude[0][mask],
- self.magnitude[1][mask],
- self.magnitude[2][mask]], -1)
+ return np.reshape([self.field[0][mask],
+ self.field[1][mask],
+ self.field[2][mask]], -1)
else:
- return self.mag_vec
+ return self.field_vec
def set_vector(self, vector, mask=None):
- """Set the magnetic components of the masked pixels to the values specified by `vector`.
+ """Set the field components of the masked pixels to the values specified by `vector`.
Parameters
----------
mask : :class:`~numpy.ndarray` (N=3, boolean), optional
Masks the pixels from which the components should be taken.
vector : :class:`~numpy.ndarray` (N=1)
- The vector containing magnetization components of the specified pixels.
+ The vector containing vector field components of the specified pixels.
Order is: first all `x`-, then all `y-, then all `z`-components.
Returns
@@ -352,129 +530,129 @@ class MagData(object):
assert np.size(vector) % 3 == 0, 'Vector has to contain all 3 components for every pixel!'
count = np.size(vector) // 3
if mask is not None:
- self.magnitude[0][mask] = vector[:count] # x-component
- self.magnitude[1][mask] = vector[count:2 * count] # y-component
- self.magnitude[2][mask] = vector[2 * count:] # z-component
+ self.field[0][mask] = vector[:count] # x-component
+ self.field[1][mask] = vector[count:2 * count] # y-component
+ self.field[2][mask] = vector[2 * count:] # z-component
else:
- self.mag_vec = vector
-
- def get_magslice(self, ax_slice=0, proj_axis='z', mode='complex'):
- """Extract a slice from the :class:`~.MagData` object.
-
- Parameters
- ----------
- proj_axis : {'z', 'y', 'x'}, optional
- The axis, from which the slice is taken. The default is 'z'.
- ax_slice : int, optional
- The slice-index of the axis specified in `proj_axis`. Defaults to zero (first slice).
- mode : {'complex', 'amplitude'}, optional
- Determines if the 2D magnetization is returned as complex values or if the amplitude
- of the two components is calculated.
-
- Returns
- -------
- mag_slice : :class:`~numpy.ndarray` (N=2)
- The extracted magnetization slice.
-
- """
- self._log.debug('Calling get_mag_slice')
- # Find slice:
- assert proj_axis == 'z' or proj_axis == 'y' or proj_axis == 'x', \
- 'Axis has to be x, y or z (as string).'
- if proj_axis == 'z': # Slice of the xy-plane with z = ax_slice
- self._log.debug('proj_axis == z')
- u_mag = np.copy(self.magnitude[0][ax_slice, ...]) # x-component
- v_mag = np.copy(self.magnitude[1][ax_slice, ...]) # y-component
- elif proj_axis == 'y': # Slice of the xz-plane with y = ax_slice
- self._log.debug('proj_axis == y')
- u_mag = np.copy(self.magnitude[0][:, ax_slice, :]) # x-component
- v_mag = np.copy(self.magnitude[2][:, ax_slice, :]) # z-component
- elif proj_axis == 'x': # Slice of the yz-plane with x = ax_slice
- self._log.debug('proj_axis == x')
- u_mag = np.swapaxes(np.copy(self.magnitude[2][..., ax_slice]), 0, 1) # z-component
- v_mag = np.swapaxes(np.copy(self.magnitude[1][..., ax_slice]), 0, 1) # y-component
- else:
- raise ValueError('{} is not a valid argument (use x, y or z)'.format(proj_axis))
- # Create data field:
- if mode == 'complex':
- return u_mag + 1j * v_mag
- elif mode == 'amplitude':
- return np.hypot(u_mag, v_mag)
- else:
- raise ValueError('Given mode not understood!')
+ self.field_vec = vector
def flip(self, axis='x'):
- """Flip/mirror the magnetization around the specified axis.
+ """Flip/mirror the vector field around the specified axis.
Parameters
----------
axis: {'x', 'y', 'z'}, optional
- The axis around which the magnetization is flipped.
+ The axis around which the vector field is flipped.
Returns
-------
- mag_data_flip: :class:`~.MagData`
- A flipped copy of the :class:`~.MagData` object.
+ mag_data_flip: :class:`~.VectorData`
+ A flipped copy of the :class:`~.VectorData` object.
"""
self._log.debug('Calling flip')
if axis == 'x':
- mag_x, mag_y, mag_z = self.magnitude[:, :, :, ::-1]
- magnitude_flip = np.array((-mag_x, mag_y, mag_z))
+ mag_x, mag_y, mag_z = self.field[:, :, :, ::-1]
+ field_flip = np.array((-mag_x, mag_y, mag_z))
elif axis == 'y':
- mag_x, mag_y, mag_z = self.magnitude[:, :, ::-1, :]
- magnitude_flip = np.array((mag_x, -mag_y, mag_z))
+ mag_x, mag_y, mag_z = self.field[:, :, ::-1, :]
+ field_flip = np.array((mag_x, -mag_y, mag_z))
elif axis == 'z':
- mag_x, mag_y, mag_z = self.magnitude[:, ::-1, :, :]
- magnitude_flip = np.array((mag_x, mag_y, -mag_z))
+ mag_x, mag_y, mag_z = self.field[:, ::-1, :, :]
+ field_flip = np.array((mag_x, mag_y, -mag_z))
else:
raise ValueError("Wrong input! 'x', 'y', 'z' allowed!")
- return MagData(self.a, magnitude_flip)
+ return VectorData(self.a, field_flip)
def rot90(self, axis='x'):
- """Rotate the magnetization 90° around the specified axis (right hand rotation).
+ """Rotate the vector field 90° around the specified axis (right hand rotation).
Parameters
----------
axis: {'x', 'y', 'z'}, optional
- The axis around which the magnetization is rotated.
+ The axis around which the vector field is rotated.
Returns
-------
- mag_data_rot: :class:`~.MagData`
- A rotated copy of the :class:`~.MagData` object.
+ mag_data_rot: :class:`~.VectorData`
+ A rotated copy of the :class:`~.VectorData` object.
"""
self._log.debug('Calling rot90')
if axis == 'x':
- magnitude_rot = np.zeros((3, self.dim[1], self.dim[0], self.dim[2]))
+ field_rot = np.zeros((3, self.dim[1], self.dim[0], self.dim[2]))
for i in range(self.dim[2]):
- mag_x, mag_y, mag_z = self.magnitude[:, :, :, i]
+ mag_x, mag_y, mag_z = self.field[:, :, :, i]
mag_xrot, mag_yrot, mag_zrot = np.rot90(mag_x), np.rot90(mag_y), np.rot90(mag_z)
- magnitude_rot[:, :, :, i] = np.array((mag_xrot, mag_zrot, -mag_yrot))
+ field_rot[:, :, :, i] = np.array((mag_xrot, mag_zrot, -mag_yrot))
elif axis == 'y':
- magnitude_rot = np.zeros((3, self.dim[2], self.dim[1], self.dim[0]))
+ field_rot = np.zeros((3, self.dim[2], self.dim[1], self.dim[0]))
for i in range(self.dim[1]):
- mag_x, mag_y, mag_z = self.magnitude[:, :, i, :]
+ mag_x, mag_y, mag_z = self.field[:, :, i, :]
mag_xrot, mag_yrot, mag_zrot = np.rot90(mag_x), np.rot90(mag_y), np.rot90(mag_z)
- magnitude_rot[:, :, i, :] = np.array((mag_zrot, mag_yrot, -mag_xrot))
+ field_rot[:, :, i, :] = np.array((mag_zrot, mag_yrot, -mag_xrot))
elif axis == 'z':
- magnitude_rot = np.zeros((3, self.dim[0], self.dim[2], self.dim[1]))
+ field_rot = np.zeros((3, self.dim[0], self.dim[2], self.dim[1]))
for i in range(self.dim[0]):
- mag_x, mag_y, mag_z = self.magnitude[:, i, :, :]
+ mag_x, mag_y, mag_z = self.field[:, i, :, :]
mag_xrot, mag_yrot, mag_zrot = np.rot90(mag_x), np.rot90(mag_y), np.rot90(mag_z)
- magnitude_rot[:, i, :, :] = np.array((mag_yrot, -mag_xrot, mag_zrot))
+ field_rot[:, i, :, :] = np.array((mag_yrot, -mag_xrot, mag_zrot))
else:
raise ValueError("Wrong input! 'x', 'y', 'z' allowed!")
- return MagData(self.a, magnitude_rot)
+ return VectorData(self.a, field_rot)
+
+ def get_slice(self, ax_slice=0, proj_axis='z', mode='complex'):
+ """Extract a slice from the :class:`~.VectorData` object.
+
+ Parameters
+ ----------
+ proj_axis : {'z', 'y', 'x'}, optional
+ The axis, from which the slice is taken. The default is 'z'.
+ ax_slice : int, optional
+ The slice-index of the axis specified in `proj_axis`. Defaults to zero (first slice).
+ mode : {'complex', 'amplitude'}, optional
+ Determines if the 2D vector field is returned as complex values or if the amplitude
+ of the two components is calculated.
+
+ Returns
+ -------
+ mag_slice : :class:`~numpy.ndarray` (N=2)
+ The extracted vector field slice.
+
+ """
+ self._log.debug('Calling get_slice')
+ # Find slice:
+ assert proj_axis == 'z' or proj_axis == 'y' or proj_axis == 'x', \
+ 'Axis has to be x, y or z (as string).'
+ if proj_axis == 'z': # Slice of the xy-plane with z = ax_slice
+ self._log.debug('proj_axis == z')
+ u_mag = np.copy(self.field[0][ax_slice, ...]) # x-component
+ v_mag = np.copy(self.field[1][ax_slice, ...]) # y-component
+ elif proj_axis == 'y': # Slice of the xz-plane with y = ax_slice
+ self._log.debug('proj_axis == y')
+ u_mag = np.copy(self.field[0][:, ax_slice, :]) # x-component
+ v_mag = np.copy(self.field[2][:, ax_slice, :]) # z-component
+ elif proj_axis == 'x': # Slice of the yz-plane with x = ax_slice
+ self._log.debug('proj_axis == x')
+ u_mag = np.swapaxes(np.copy(self.field[2][..., ax_slice]), 0, 1) # z-component
+ v_mag = np.swapaxes(np.copy(self.field[1][..., ax_slice]), 0, 1) # y-component
+ else:
+ raise ValueError('{} is not a valid argument (use x, y or z)'.format(proj_axis))
+ # Create data field:
+ if mode == 'complex':
+ return u_mag + 1j * v_mag
+ elif mode == 'amplitude':
+ return np.hypot(u_mag, v_mag)
+ else:
+ raise ValueError('Given mode not understood!')
def to_signal(self):
- """Convert :class:`~.MagData` data into a HyperSpy signal.
+ """Convert :class:`~.VectorData` data into a HyperSpy signal.
Returns
-------
signal: :class:`~hyperspy.signals.Signal`
- Representation of the :class:`~.MagData` object as a HyperSpy Signal.
+ Representation of the :class:`~.VectorData` object as a HyperSpy Signal.
Notes
-----
@@ -487,7 +665,7 @@ class MagData(object):
self._log.error('This method recquires the hyperspy package!')
return
# Create signal:
- signal = hs.signals.Signal(np.rollaxis(self.magnitude, 0, 4))
+ signal = hs.signals.Signal(np.rollaxis(self.field, 0, 4))
# Set axes:
signal.axes_manager[0].name = 'x-axis'
signal.axes_manager[0].units = 'nm'
@@ -501,23 +679,23 @@ class MagData(object):
signal.axes_manager[3].name = 'components (x,y,z)'
signal.axes_manager[3].units = ''
# Set metadata:
- signal.metadata.Signal.title = 'MagData'
+ signal.metadata.Signal.title = 'VectorData'
# Return signal:
return signal
@classmethod
def from_signal(cls, signal):
- """Convert a :class:`~hyperspy.signals.Signal` object to a :class:`~.MagData` object.
+ """Convert a :class:`~hyperspy.signals.Signal` object to a :class:`~.FieldData` object.
Parameters
----------
signal: :class:`~hyperspy.signals.Signal`
- The :class:`~hyperspy.signals.Signal` object which should be converted to MagData.
+ The :class:`~hyperspy.signals.Signal` object which should be converted to FieldData.
Returns
-------
- mag_data: :class:`~.MagData`
- A :class:`~.MagData` object containing the loaded data.
+ mag_data: :class:`~.FieldData`
+ A :class:`~.VectorData` object containing the loaded data.
Notes
-----
@@ -525,20 +703,20 @@ class MagData(object):
"""
cls._log.debug('Calling from_signal')
- # Extract magnitude:
- magnitude = np.rollaxis(signal.data, 3, 0)
+ # Extract field:
+ field = np.rollaxis(signal.data, 3, 0)
# Extract properties:
a = signal.axes_manager[0].scale
- return cls(a, magnitude)
+ return cls(a, field)
- def save_to_hdf5(self, filename='magdata.hdf5'):
- """Save magnetization data in a file with HyperSpys HDF5-format.
+ def save_to_hdf5(self, filename='vecdata.hdf5'):
+ """Save vector field data in a file with HyperSpys HDF5-format.
Parameters
----------
filename : string, optional
- The name of the HDF5-file in which to store the magnetization data.
- The default is 'magdata.hdf5'.
+ The name of the HDF5-file in which to store the vector field.
+ The default is 'vecdata.hdf5'.
Returns
-------
@@ -549,7 +727,7 @@ class MagData(object):
# Construct path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid.config import DIR_FILES
- directory = os.path.join(DIR_FILES, 'magdata')
+ directory = os.path.join(DIR_FILES, 'vecdata')
if not os.path.exists(directory):
os.makedirs(directory)
filename = os.path.join(directory, filename)
@@ -558,7 +736,7 @@ class MagData(object):
@classmethod
def load_from_hdf5(cls, filename):
- """Construct :class:`~.MagData` object from HyperSpys HDF5-file.
+ """Construct :class:`~.VectorData` object from HyperSpys HDF5-file.
Parameters
----------
@@ -567,8 +745,8 @@ class MagData(object):
Returns
-------
- mag_data: :class:`~.MagData`
- A :class:`~.MagData` object containing the loaded data.
+ mag_data: :class:`~.VectorData`
+ A :class:`~.VectorData` object containing the loaded data.
"""
cls._log.debug('Calling load_from_hdf5')
@@ -578,19 +756,19 @@ class MagData(object):
# Use relative path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid.config import DIR_FILES
- directory = os.path.join(DIR_FILES, 'magdata')
+ directory = os.path.join(DIR_FILES, 'vecdata')
filename = os.path.join(directory, filename)
# Load data from file:
- return MagData.from_signal(hs.load(filename))
+ return VectorData.from_signal(hs.load(filename))
- def save_to_llg(self, filename='magdata.txt'):
- """Save magnetization data in a file with LLG-format.
+ def save_to_llg(self, filename='vecdata.txt'):
+ """Save vector field data in a file with LLG-format.
Parameters
----------
filename : string, optional
- The name of the LLG-file in which to store the magnetization data.
- The default is '..\output\magdata_output.txt'.
+ The name of the LLG-file in which to store the vector field data.
+ The default is 'vecdata.txt'.
Returns
-------
@@ -599,14 +777,14 @@ class MagData(object):
"""
self._log.debug('Calling save_to_llg')
SCALE = 1.0E-9 / 1.0E-2 # from nm to cm
- # Create 3D meshgrid and reshape it and the magnetization into a list where x varies first:
+ # Create 3D meshgrid and reshape it and the field into a list where x varies first:
zz, yy, xx = self.a * SCALE * (np.indices(self.dim) + 0.5).reshape(3, -1)
- x_vec, y_vec, z_vec = self.magnitude.reshape(3, -1)
+ x_vec, y_vec, z_vec = self.field.reshape(3, -1)
data = np.array([xx, yy, zz, x_vec, y_vec, z_vec]).T
# Construct path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid.config import DIR_FILES
- directory = os.path.join(DIR_FILES, 'magdata')
+ directory = os.path.join(DIR_FILES, 'vecdata')
if not os.path.exists(directory):
os.makedirs(directory)
filename = os.path.join(directory, filename)
@@ -619,7 +797,7 @@ class MagData(object):
@classmethod
def load_from_llg(cls, filename):
- """Construct :class:`~.MagData` object from LLG-file.
+ """Construct :class:`~.VectorData` object from LLG-file.
Parameters
----------
@@ -628,8 +806,8 @@ class MagData(object):
Returns
-------
- mag_data: :class:`~.MagData`
- A :class:`~.MagData` object containing the loaded data.
+ mag_data: :class:`~.VectorData`
+ A :class:`~.VectorData` object containing the loaded data.
"""
cls._log.debug('Calling load_from_llg')
@@ -637,19 +815,19 @@ class MagData(object):
# Use relative path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid.config import DIR_FILES
- directory = os.path.join(DIR_FILES, 'magdata')
+ directory = os.path.join(DIR_FILES, 'vecdata')
filename = os.path.join(directory, filename)
# Load data from file:
data = np.genfromtxt(filename, skip_header=2)
dim = tuple(np.genfromtxt(filename, dtype=int, skip_header=1, skip_footer=len(data[:, 0])))
a = (data[1, 0] - data[0, 0]) / SCALE
- magnitude = data[:, 3:6].T.reshape((3,) + dim)
- return cls(a, magnitude)
+ field = data[:, 3:6].T.reshape((3,) + dim)
+ return cls(a, field)
- def quiver_plot(self, title='Magnetization Distribution', axis=None, proj_axis='z',
+ def quiver_plot(self, title='Vector Field', axis=None, proj_axis='z',
coloring='angle', ar_dens=1, ax_slice=None, log=False, scaled=True,
scale=1., show_mask=True):
- """Plot a slice of the magnetization as a quiver plot.
+ """Plot a slice of the vector field as a quiver plot.
Parameters
----------
@@ -692,8 +870,8 @@ class MagData(object):
if ax_slice is None:
self._log.debug('ax_slice is None')
ax_slice = self.dim[0] // 2
- u_mag = np.copy(self.magnitude[0][ax_slice, ...]) # x-component
- v_mag = np.copy(self.magnitude[1][ax_slice, ...]) # y-component
+ u_mag = np.copy(self.field[0][ax_slice, ...]) # x-component
+ v_mag = np.copy(self.field[1][ax_slice, ...]) # y-component
u_label = 'x [px]'
v_label = 'y [px]'
submask = self.get_mask()[ax_slice, ...]
@@ -702,8 +880,8 @@ class MagData(object):
if ax_slice is None:
self._log.debug('ax_slice is None')
ax_slice = self.dim[1] // 2
- u_mag = np.copy(self.magnitude[0][:, ax_slice, :]) # x-component
- v_mag = np.copy(self.magnitude[2][:, ax_slice, :]) # z-component
+ u_mag = np.copy(self.field[0][:, ax_slice, :]) # x-component
+ v_mag = np.copy(self.field[2][:, ax_slice, :]) # z-component
u_label = 'x [px]'
v_label = 'z [px]'
submask = self.get_mask()[:, ax_slice, :]
@@ -712,8 +890,8 @@ class MagData(object):
if ax_slice is None:
self._log.debug('ax_slice is None')
ax_slice = self.dim[2] // 2
- u_mag = np.swapaxes(np.copy(self.magnitude[2][..., ax_slice]), 0, 1) # z-component
- v_mag = np.swapaxes(np.copy(self.magnitude[1][..., ax_slice]), 0, 1) # y-component
+ u_mag = np.swapaxes(np.copy(self.field[2][..., ax_slice]), 0, 1) # z-component
+ v_mag = np.swapaxes(np.copy(self.field[1][..., ax_slice]), 0, 1) # y-component
u_label = 'z [px]'
v_label = 'y [px]'
submask = self.get_mask()[..., ax_slice]
@@ -759,7 +937,7 @@ class MagData(object):
v_mag = np.round(v_mag, decimals=cutoff) / min_value
v_mag = np.log10(np.abs(v_mag) + 1) * np.sign(v_mag)
amplitudes = np.hypot(u_mag, v_mag) # Recalculate (used if scaled)!
- # Scale the magnitude of the arrows to the highest one (if specified):
+ # Scale the amplitude of the arrows to the highest one (if specified):
if scaled:
u_mag /= amplitudes.max() + 1E-30
v_mag /= amplitudes.max() + 1E-30
@@ -784,16 +962,16 @@ class MagData(object):
# Return plotting axis:
return axis
- def quiver_plot3d(self, title='Magnetization Distribution', limit=None, cmap='jet',
+ def quiver_plot3d(self, title='Vector Field', limit=None, cmap='jet',
mode='2darrow', coloring='angle', ar_dens=1, opacity=1.0):
- """Plot the magnetization as 3D-vectors in a quiverplot.
+ """Plot the vector field as 3D-vectors in a quiverplot.
Parameters
----------
title : string, optional
The title for the plot.
limit : float, optional
- Plotlimit for the magnetization arrow length used to scale the colormap.
+ Plotlimit for the vector field arrow length used to scale the colormap.
cmap : string, optional
String describing the colormap which is used (default is 'jet').
ar_dens: int (optional)
@@ -818,16 +996,16 @@ class MagData(object):
a = self.a
dim = self.dim
if limit is None:
- limit = np.max(self.mag_amp)
+ limit = np.max(self.field_amp)
ad = ar_dens
# Create points and vector components as lists:
zzz, yyy, xxx = (np.indices(dim) - a / 2).reshape((3,) + dim)
zzz = zzz[::ad, ::ad, ::ad].flatten()
yyy = yyy[::ad, ::ad, ::ad].flatten()
xxx = xxx[::ad, ::ad, ::ad].flatten()
- x_mag = self.magnitude[0][::ad, ::ad, ::ad].flatten()
- y_mag = self.magnitude[1][::ad, ::ad, ::ad].flatten()
- z_mag = self.magnitude[2][::ad, ::ad, ::ad].flatten()
+ x_mag = self.field[0][::ad, ::ad, ::ad].flatten()
+ y_mag = self.field[1][::ad, ::ad, ::ad].flatten()
+ z_mag = self.field[2][::ad, ::ad, ::ad].flatten()
# Plot them as vectors:
mlab.figure(size=(750, 700))
plot = mlab.quiver3d(xxx, yyy, zzz, x_mag, y_mag, z_mag,
@@ -854,39 +1032,243 @@ class MagData(object):
mlab.axes(plot)
mlab.title(title, height=0.95, size=0.35)
mlab.orientation_axes()
- # mlab.show()
return plot
- def contour_plot3d(self, title='Magnetization Distribution', contours=10, opacity=0.25):
- """Plot the magnetization as 3D-vectors in a quiverplot.
+
+class ScalarData(FieldData):
+ """Class for storing scalar field data.
+
+ Represents 3-dimensional scalar field distributions which is stored as a 3-dimensional
+ numpy array in `field`, but which can also be accessed as a vector via `field_vec`.
+ :class:`~.ScalarData` objects support negation, arithmetic operators (``+``, ``-``, ``*``)
+ and their augmented counterparts (``+=``, ``-=``, ``*=``), with numbers and other
+ :class:`~.ScalarData` objects, if their dimensions and grid spacings match. It is possible
+ to load data from HDF5 or LLG (.txt) files or to save the data in these formats.
+ Plotting methods are also provided.
+
+ Attributes
+ ----------
+ a: float
+ The grid spacing in nm.
+ field: :class:`~numpy.ndarray` (N=4)
+ The scalar field.
+
+ """
+ _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.
Parameters
----------
- title: string, optional
- The title for the plot.
- contours: int, optional
- Number of contours which should be plotted.
- opacity: float, optional
- Defines the opacity of the contours. Default is 0.25.
+ n : int, optional
+ Number of times the field distribution is scaled down. The default is 1.
Returns
-------
- plot : :class:`mayavi.modules.vectors.Vectors`
- The plot object.
+ None
+ Notes
+ -----
+ Acts in place and changes dimensions and grid spacing accordingly.
+ Only possible, if each axis length is a power of 2!
"""
- self._log.debug('Calling quiver_plot3D')
- from mayavi import mlab
- # Create points and vector components as lists:
- x_mag, y_mag, z_mag = self.magnitude
- amplitudes = np.sqrt(x_mag ** 2 + y_mag ** 2 + z_mag ** 2)
- # Plot them as vectors:
- mlab.figure(size=(750, 700))
- plot = mlab.contour3d(amplitudes, contours=contours, opacity=opacity)
- mlab.outline(plot)
- mlab.axes(plot)
- mlab.title(title, height=0.95, size=0.35)
- mlab.orientation_axes()
- # mlab.show()
- return plot
+ self._log.debug('Calling scale_down')
+ assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
+ self.a *= 2 ** n
+ for t in range(n):
+ # Pad if necessary:
+ pz, py, px = self.dim[0] % 2, self.dim[1] % 2, self.dim[2] % 2
+ if pz != 0 or py != 0 or px != 0:
+ self.field = np.pad(self.field, ((0, pz), (0, py), (0, px)), mode='constant')
+ # Create coarser grid for the field:
+ shape_4d = (self.dim[0] / 2, 2, self.dim[1] / 2, 2, self.dim[2] / 2, 2)
+ self.field = self.field.reshape(shape_4d).mean(axis=(5, 3, 1))
+
+ def scale_up(self, n=1, order=0):
+ """Scale up the field distribution using spline interpolation of the requested order.
+
+ Parameters
+ ----------
+ n : int, optional
+ Power of 2 with which the grid is scaled. Default is 1, which means every axis is
+ increased by a factor of ``2**1 = 2``.
+ order : int, optional
+ The order of the spline interpolation, which has to be in the range between 0 and 5
+ and defaults to 0.
+
+ Returns
+ -------
+ None
+
+ Notes
+ -----
+ 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)), \
+ 'order must be a positive integer between 0 and 5!'
+ self.a /= 2 ** n
+ self.field = zoom(self.field, zoom=2 ** n, order=order)
+
+ def get_vector(self, mask):
+ """Returns the field as a vector, specified by a mask.
+
+ Parameters
+ ----------
+ mask : :class:`~numpy.ndarray` (N=3, boolean)
+ Masks the pixels from which the components should be taken.
+
+ Returns
+ -------
+ vector : :class:`~numpy.ndarray` (N=1)
+ The vector containing the field of the specified pixels.
+
+ """
+ self._log.debug('Calling get_vector')
+ if mask is not None:
+ return np.reshape(self.field[mask], -1)
+ else:
+ return self.field_vec
+
+ def set_vector(self, vector, mask=None):
+ """Set the field components of the masked pixels to the values specified by `vector`.
+
+ Parameters
+ ----------
+ mask : :class:`~numpy.ndarray` (N=3, boolean), optional
+ Masks the pixels from which the components should be taken.
+ vector : :class:`~numpy.ndarray` (N=1)
+ The vector containing the field of the specified pixels.
+
+ Returns
+ -------
+ None
+
+ """
+ self._log.debug('Calling set_vector')
+ vector = np.asarray(vector, dtype=fft.FLOAT)
+ if mask is not None:
+ self.field[mask] = vector
+ else:
+ self.field_vec = vector
+
+ def to_signal(self):
+ """Convert :class:`~.ScalarData` data into a HyperSpy signal.
+
+ Returns
+ -------
+ signal: :class:`~hyperspy.signals.Signal`
+ Representation of the :class:`~.ScalarData` object as a HyperSpy Signal.
+
+ Notes
+ -----
+ This method recquires the hyperspy package!
+
+ """
+ self._log.debug('Calling to_signal')
+ # Try importing HyperSpy:
+ if hs is None:
+ self._log.error('This method recquires the hyperspy package!')
+ return
+ # Create signal:
+ signal = hs.signals.Signal(self.field)
+ # Set axes:
+ signal.axes_manager[0].name = 'x-axis'
+ signal.axes_manager[0].units = 'nm'
+ signal.axes_manager[0].scale = self.a
+ signal.axes_manager[1].name = 'y-axis'
+ signal.axes_manager[1].units = 'nm'
+ signal.axes_manager[1].scale = self.a
+ signal.axes_manager[2].name = 'z-axis'
+ signal.axes_manager[2].units = 'nm'
+ signal.axes_manager[2].scale = self.a
+ # Set metadata:
+ signal.metadata.Signal.title = 'ScalarData'
+ # Return signal:
+ return signal
+
+ @classmethod
+ def from_signal(cls, signal):
+ """Convert a :class:`~hyperspy.signals.Signal` object to a :class:`~.ScalarData` object.
+
+ Parameters
+ ----------
+ signal: :class:`~hyperspy.signals.Signal`
+ The :class:`~hyperspy.signals.Signal` object which should be converted to ScalarData.
+
+ Returns
+ -------
+ mag_data: :class:`~.ScalarData`
+ A :class:`~.ScalarData` object containing the loaded data.
+
+ Notes
+ -----
+ This method recquires the hyperspy package!
+
+ """
+ cls._log.debug('Calling from_signal')
+ # Extract field:
+ field = signal.data
+ # Extract properties:
+ a = signal.axes_manager[0].scale
+ return cls(a, field)
+
+ def save_to_hdf5(self, filename='scaldata.hdf5'):
+ """Save field data in a file with HyperSpys HDF5-format.
+
+ Parameters
+ ----------
+ filename : string, optional
+ The name of the HDF5-file in which to store the field data.
+ The default is 'scaldata.hdf5'.
+
+ Returns
+ -------
+ None
+
+ """
+ self._log.debug('Calling save_to_hdf5')
+ # Construct path if filename isn't already absolute:
+ if not os.path.isabs(filename):
+ from pyramid.config import DIR_FILES
+ directory = os.path.join(DIR_FILES, 'scaldata')
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+ filename = os.path.join(directory, filename)
+ # Save data to file:
+ self.to_signal().save(filename)
+
+ @classmethod
+ def load_from_hdf5(cls, filename):
+ """Construct :class:`~.ScalarData` object from HyperSpys HDF5-file.
+
+ Parameters
+ ----------
+ filename : string
+ The name of the HDF5-file from which to load the data. Standard format is '\*.hdf5'.
+
+ Returns
+ -------
+ mag_data: :class:`~.ScalarData`
+ A :class:`~.ScalarData` object containing the loaded data.
+
+ """
+ cls._log.debug('Calling load_from_hdf5')
+ if hs is None:
+ cls._log.error('This method recquires the hyperspy package!')
+ return
+ # Use relative path if filename isn't already absolute:
+ if not os.path.isabs(filename):
+ from pyramid.config import DIR_FILES
+ directory = os.path.join(DIR_FILES, 'scaldata')
+ filename = os.path.join(directory, filename)
+ # Load data from file:
+ return ScalarData.from_signal(hs.load(filename))
diff --git a/pyramid/forwardmodel.py b/pyramid/forwardmodel.py
index f3e97fe79b1eb6b496bdc8033b02c4bf4477ac24..eca8aca8a9b60220692746db9011a2627127a8e3 100644
--- a/pyramid/forwardmodel.py
+++ b/pyramid/forwardmodel.py
@@ -14,7 +14,7 @@ import sys
import numpy as np
from pyramid.dataset import DataSet
-from pyramid.magdata import MagData
+from pyramid.fielddata import VectorData
from pyramid.ramp import Ramp
__all__ = ['ForwardModel', 'DistributedForwardModel']
@@ -59,7 +59,7 @@ class ForwardModel(object):
self.n += self.ramp.n
self.shape = (self.m, self.n)
self.hook_points = data_set.hook_points
- self.mag_data = MagData(self.data_set.a, np.zeros((3,) + self.data_set.dim))
+ self.mag_data = VectorData(self.data_set.a, np.zeros((3,) + self.data_set.dim))
self._log.debug('Creating ' + str(self))
def __repr__(self):
@@ -74,7 +74,7 @@ class ForwardModel(object):
# Extract ramp parameters if necessary (x will be shortened!):
x = self.ramp.extract_ramp_params(x)
# Reset mag_data and fill with vector:
- self.mag_data.magnitude[...] = 0
+ self.mag_data.field[...] = 0
self.mag_data.set_vector(x, self.data_set.mask)
# Simulate all phase maps and create result vector:
result = np.zeros(self.m)
@@ -110,13 +110,13 @@ class ForwardModel(object):
# Extract ramp parameters if necessary (vector will be shortened!):
vector = self.ramp.extract_ramp_params(vector)
# Reset mag_data and fill with vector:
- self.mag_data.magnitude[...] = 0
+ self.mag_data.field[...] = 0
self.mag_data.set_vector(vector, self.data_set.mask)
# Simulate all phase maps and create result vector:
result = np.zeros(self.m)
hp = self.hook_points
for i, projector in enumerate(self.data_set.projectors):
- mag_vec = self.mag_data.mag_vec
+ mag_vec = self.mag_data.field_vec
mapper = self.phase_mappers[projector.dim_uv]
res = mapper.jac_dot(projector.jac_dot(mag_vec))
res += self.ramp.jac_dot(i) # add ramp!
@@ -148,7 +148,7 @@ class ForwardModel(object):
sub_vec = vector[hp[i]:hp[i + 1]]
mapper = self.phase_mappers[projector.dim_uv]
proj_T_result += projector.jac_T_dot(mapper.jac_T_dot(sub_vec))
- self.mag_data.mag_vec = proj_T_result
+ self.mag_data.field_vec = proj_T_result
result = self.mag_data.get_vector(self.data_set.mask)
ramp_params = self.ramp.jac_T_dot(vector) # calculate ramp_params separately!
return np.concatenate((result, ramp_params))
diff --git a/pyramid/magcreator.py b/pyramid/magcreator.py
index a228a133792cef9c0c57f55fb196de0af45a7253..20d31d4dc8f06ab7557352771927a3978807d26e 100644
--- a/pyramid/magcreator.py
+++ b/pyramid/magcreator.py
@@ -34,7 +34,7 @@ class Shapes(object):
The :class:`~.Shapes` class is a collection of some methods that return a 3-dimensional
matrix that represents the magnetized volume and consists of values between 0 and 1.
This matrix is used in the functions of the :mod:`~.magcreator` module to create
- :class:`~pyramid.magdata.MagData` objects which store the magnetic informations.
+ :class:`~pyramid.magdata.VectorData` objects which store the magnetic informations.
"""
@@ -274,7 +274,7 @@ class Shapes(object):
return mag_shape
-def create_mag_dist_homog(mag_shape, phi, theta=pi / 2, magnitude=1):
+def create_mag_dist_homog(mag_shape, phi, theta=pi / 2, amplitude=1):
"""Create a 3-dimensional magnetic distribution of a homogeneously magnetized object.
Parameters
@@ -286,12 +286,12 @@ def create_mag_dist_homog(mag_shape, phi, theta=pi / 2, magnitude=1):
theta : float, optional
The polar angle, describing the direction of the magnetized object.
The default is pi/2, which means, the z-component is zero.
- magnitude : float, optional
- The relative magnitude for the magnetic shape. The default is 1.
+ amplitude : float, optional
+ The relative amplitude for the magnetic shape. The default is 1.
Returns
-------
- magnitude : tuple (N=3) of :class:`~numpy.ndarray` (N=3)
+ amplitude : tuple (N=3) of :class:`~numpy.ndarray` (N=3)
The magnetic distribution as a tuple of the 3 components in
`x`-, `y`- and `z`-direction on the 3-dimensional grid.
@@ -299,13 +299,13 @@ def create_mag_dist_homog(mag_shape, phi, theta=pi / 2, magnitude=1):
_log.debug('Calling create_mag_dist_homog')
dim = np.shape(mag_shape)
assert len(dim) == 3, 'Magnetic shapes must describe 3-dimensional distributions!'
- z_mag = np.ones(dim) * np.cos(theta) * mag_shape * magnitude
- y_mag = np.ones(dim) * np.sin(theta) * np.sin(phi) * mag_shape * magnitude
- x_mag = np.ones(dim) * np.sin(theta) * np.cos(phi) * mag_shape * magnitude
+ z_mag = np.ones(dim) * np.cos(theta) * mag_shape * amplitude
+ y_mag = np.ones(dim) * np.sin(theta) * np.sin(phi) * mag_shape * amplitude
+ x_mag = np.ones(dim) * np.sin(theta) * np.cos(phi) * mag_shape * amplitude
return np.array([x_mag, y_mag, z_mag])
-def create_mag_dist_vortex(mag_shape, center=None, axis='z', magnitude=1):
+def create_mag_dist_vortex(mag_shape, center=None, axis='z', amplitude=1):
"""Create a 3-dimensional magnetic distribution of a homogeneous magnetized object.
Parameters
@@ -316,15 +316,15 @@ def create_mag_dist_vortex(mag_shape, center=None, axis='z', magnitude=1):
The vortex center, given in 2D `(v, u)` or 3D `(z, y, x)`, where the perpendicular axis
is is discarded. Is set to the center of the field of view if not specified. The vortex
center has to be between two pixels.
- magnitude : float, optional
- The relative magnitude for the magnetic shape. The default is 1. Negative signs reverse
+ amplitude : float, optional
+ The relative amplitude for the magnetic shape. The default is 1. Negative signs reverse
the vortex direction (left-handed instead of right-handed).
axis : {'z', 'y', 'x'}, optional
The orientation of the vortex axis. The default is 'z'.
Returns
-------
- magnitude : tuple (N=3) of :class:`~numpy.ndarray` (N=3)
+ amplitude : tuple (N=3) of :class:`~numpy.ndarray` (N=3)
The magnetic distribution as a tuple of the 3 components in
`x`-, `y`- and `z`-direction on the 3-dimensional grid.
@@ -352,8 +352,8 @@ def create_mag_dist_vortex(mag_shape, center=None, axis='z', magnitude=1):
phi = np.expand_dims(np.arctan2(vv, uu) - pi / 2, axis=0)
phi = np.tile(phi, (dim[0], 1, 1))
z_mag = np.zeros(dim)
- y_mag = -np.ones(dim) * np.sin(phi) * mag_shape * magnitude
- x_mag = -np.ones(dim) * np.cos(phi) * mag_shape * magnitude
+ y_mag = -np.ones(dim) * np.sin(phi) * mag_shape * amplitude
+ x_mag = -np.ones(dim) * np.cos(phi) * mag_shape * amplitude
elif axis == 'y':
if len(center) == 3: # if a 3D-center is given, just take the x and z components
center = (center[0], center[2])
@@ -362,9 +362,9 @@ def create_mag_dist_vortex(mag_shape, center=None, axis='z', magnitude=1):
uu, vv = np.meshgrid(u, v)
phi = np.expand_dims(np.arctan2(vv, uu) - pi / 2, axis=1)
phi = np.tile(phi, (1, dim[1], 1))
- z_mag = np.ones(dim) * np.sin(phi) * mag_shape * magnitude
+ z_mag = np.ones(dim) * np.sin(phi) * mag_shape * amplitude
y_mag = np.zeros(dim)
- x_mag = np.ones(dim) * np.cos(phi) * mag_shape * magnitude
+ x_mag = np.ones(dim) * np.cos(phi) * mag_shape * amplitude
elif axis == 'x':
if len(center) == 3: # if a 3D-center is given, just take the z and y components
center = (center[0], center[1])
@@ -373,8 +373,8 @@ def create_mag_dist_vortex(mag_shape, center=None, axis='z', magnitude=1):
uu, vv = np.meshgrid(u, v)
phi = np.expand_dims(np.arctan2(vv, uu) - pi / 2, axis=2)
phi = np.tile(phi, (1, 1, dim[2]))
- z_mag = -np.ones(dim) * np.sin(phi) * mag_shape * magnitude
- y_mag = -np.ones(dim) * np.cos(phi) * mag_shape * magnitude
+ z_mag = -np.ones(dim) * np.sin(phi) * mag_shape * amplitude
+ y_mag = -np.ones(dim) * np.cos(phi) * mag_shape * amplitude
x_mag = np.zeros(dim)
else:
raise ValueError('{} is not a valid argument (use x, y or z)'.format(axis))
diff --git a/pyramid/phasemap.py b/pyramid/phasemap.py
index 2e95cfaa8b7e9cc812c0049ec26fb082a3631a86..b1bc70afdb73d1b574968c9a2a3f542bd84b13d2 100644
--- a/pyramid/phasemap.py
+++ b/pyramid/phasemap.py
@@ -214,7 +214,7 @@ class PhaseMap(object):
self._log.debug('Adding two PhaseMap objects')
assert other.a == self.a, 'Added phase has to have the same grid spacing!'
assert other.phase.shape == self.dim_uv, \
- 'Added magnitude has to have the same dimensions!'
+ 'Added field has to have the same dimensions!'
mask_comb = np.logical_or(self.mask, other.mask) # masks combine
conf_comb = (self.confidence + other.confidence) / 2 # confidence averaged!
return PhaseMap(self.a, self.phase + other.phase, mask_comb, conf_comb, self.unit)
@@ -504,8 +504,8 @@ class PhaseMap(object):
Returns
-------
- mag_data: :class:`~.MagData`
- A :class:`~.MagData` object containing the loaded data.
+ mag_data: :class:`~.VectorData`
+ A :class:`~.VectorData` object containing the loaded data.
"""
cls._log.debug('Calling load_from_hdf5')
@@ -735,7 +735,7 @@ class PhaseMap(object):
holo = np.cos(gain * self.phase)
holo += 1 # Shift to positive values
holo /= 2 # Rescale to [0, 1]
- # Calculate the phase gradients, expressed by magnitude and angle:
+ # Calculate the phase gradients, expressed by amplitude and angle:
phase_grad_x, phase_grad_y = np.gradient(self.phase, self.a, self.a)
angles = (1 - np.arctan2(phase_grad_y, phase_grad_x) / np.pi) / 2
phase_grad_amp = np.hypot(phase_grad_y, phase_grad_x)
diff --git a/pyramid/phasemapper.py b/pyramid/phasemapper.py
index 2b05ed7c073bc1be9c9c8f84abbe63787dfc5cd4..b07345a1defcd64014170e8b95114952e251f555 100644
--- a/pyramid/phasemapper.py
+++ b/pyramid/phasemapper.py
@@ -16,11 +16,11 @@ from numpy import pi
from pyramid import fft
from pyramid.kernel import Kernel
-from pyramid.magdata import MagData
+from pyramid.fielddata import VectorData, ScalarData
from pyramid.phasemap import PhaseMap
from pyramid.projector import RotTiltProjector, XTiltProjector, YTiltProjector, SimpleProjector
-__all__ = ['PhaseMapperRDFC', 'PhaseMapperRDRC', 'PhaseMapperFDFC', 'pm']
+__all__ = ['PhaseMapperRDFC', 'PhaseMapperRDRC', 'PhaseMapperFDFC', 'PhaseMapperMIP', 'pm']
_log = logging.getLogger(__name__)
PHI_0 = 2067.83 # magnetic flux in T*nm²
@@ -34,10 +34,10 @@ class PhaseMapper(object):
"""Abstract base class for the phase calculation from a 2-dimensional distribution.
The :class:`~.PhaseMapper-` class represents a strategy for the phasemapping of a
- 2-dimensional magnetic distribution with two components onto a scalar phase map.
- :class:`~.Kernel` is an abstract base class and provides a unified interface which should be
- subclassed with custom :func:`__init__` and :func:`__call__` functions. Concrete subclasses
- can be called as a function and take a :class:`~.MagData` object as input and return a
+ 2-dimensional magnetic/electric distribution onto a scalar phase map. :class:`~.PhaseMapper`
+ is an abstract base class and provides a unified interface which should be subclassed with
+ custom :func:`__init__` and :func:`__call__` functions. Concrete subclasses
+ can be called as a function and take a :class:`~.FieldData` object as input and return a
:class:`~.PhaseMap` object.
"""
@@ -46,7 +46,7 @@ class PhaseMapper(object):
_log = logging.getLogger(__name__ + '.PhaseMapper')
@abc.abstractmethod
- def __call__(self, mag_data):
+ def __call__(self, field_data):
raise NotImplementedError()
@abc.abstractmethod
@@ -56,9 +56,7 @@ class PhaseMapper(object):
Parameters
----------
vector : :class:`~numpy.ndarray` (N=1)
- Vectorized form of the magnetization in `u`- and `v`-direction of every pixel
- (row-wise). The first ``N**2`` elements have to correspond to the `u`-, the next
- ``N**2`` elements to the `v`-component of the magnetization.
+ Vectorized form of the field.
Returns
-------
@@ -75,14 +73,13 @@ class PhaseMapper(object):
Parameters
----------
vector : :class:`~numpy.ndarray` (N=1)
- Vector with ``N**2`` entries which represents a matrix with dimensions like a scalar
- phasemap.
+ Vector which represents a matrix with dimensions like a scalar phasemap.
Returns
-------
result : :class:`~numpy.ndarray` (N=1)
Product of the transposed Jacobi matrix (which is not explicitely calculated) with
- the vector, which has ``2*N**2`` entries like a 2D magnetic projection.
+ the vector.
"""
raise NotImplementedError()
@@ -93,7 +90,7 @@ class PhaseMapperRDFC(PhaseMapper):
space convolution.
The :class:`~.PMConvolve` class represents a phase mapping strategy involving discretization in
- real space. It utilizes the convolution in Fourier space, directly takes :class:`~.MagData`
+ real space. It utilizes the convolution in Fourier space, directly takes :class:`~.VectorData`
objects and returns :class:`~.PhaseMap` objects.
Attributes
@@ -128,13 +125,13 @@ class PhaseMapperRDFC(PhaseMapper):
return 'PhaseMapperRDFC(kernel=%s)' % self.kernel
def __call__(self, mag_data):
- assert isinstance(mag_data, MagData), 'Only MagData objects can be mapped!'
+ assert isinstance(mag_data, VectorData), 'Only VectorData objects can be mapped!'
assert mag_data.a == self.kernel.a, 'Grid spacing has to match!'
assert mag_data.dim[0] == 1, 'Magnetic distribution must be 2-dimensional!'
assert mag_data.dim[1:3] == self.kernel.dim_uv, 'Dimensions do not match!'
# Process input parameters:
- self.u_mag[self.kernel.slice_mag] = mag_data.magnitude[0, 0, ...] # u-component
- self.v_mag[self.kernel.slice_mag] = mag_data.magnitude[1, 0, ...] # v-component
+ self.u_mag[self.kernel.slice_mag] = mag_data.field[0, 0, ...] # u-component
+ self.v_mag[self.kernel.slice_mag] = mag_data.field[1, 0, ...] # v-component
return PhaseMap(mag_data.a, self._convolve())
def _convolve(self):
@@ -201,7 +198,7 @@ class PhaseMapperRDRC(PhaseMapper):
"""Class representing a phase mapping strategy using real space discretization.
The :class:`~.PMReal` class represents a phase mapping strategy involving discretization in
- real space. It directly takes :class:`~.MagData` objects and returns :class:`~.PhaseMap`
+ real space. It directly takes :class:`~.VectorData` objects and returns :class:`~.PhaseMap`
objects.
Attributes
@@ -246,12 +243,12 @@ class PhaseMapperRDRC(PhaseMapper):
def __call__(self, mag_data):
self._log.debug('Calling __call__')
dim_uv = self.kernel.dim_uv
- assert isinstance(mag_data, MagData), 'Only MagData objects can be mapped!'
+ assert isinstance(mag_data, VectorData), 'Only VectorData objects can be mapped!'
assert mag_data.a == self.kernel.a, 'Grid spacing has to match!'
assert mag_data.dim[0] == 1, 'Magnetic distribution must be 2-dimensional!'
assert mag_data.dim[1:3] == dim_uv, 'Dimensions do not match!'
# Process input parameters:
- u_mag, v_mag = mag_data.magnitude[0:2, 0, ...]
+ u_mag, v_mag = mag_data.field[0:2, 0, ...]
# Get kernel (lookup-tables for the phase of one pixel):
u_phi = self.kernel.u
v_phi = self.kernel.v
@@ -355,7 +352,7 @@ class PhaseMapperFDFC(PhaseMapper):
The :class:`~.PMFourier` class represents a phase mapping strategy involving discretization in
Fourier space. It utilizes the Fourier transforms, which are inherently calculated in the
- :class:`~.Kernel` class and directly takes :class:`~.MagData` objects and returns
+ :class:`~.Kernel` class and directly takes :class:`~.VectorData` objects and returns
:class:`~.PhaseMap` objects.
Attributes
@@ -401,12 +398,12 @@ class PhaseMapperFDFC(PhaseMapper):
def __call__(self, mag_data):
self._log.debug('Calling __call__')
- assert isinstance(mag_data, MagData), 'Only MagData objects can be mapped!'
+ assert isinstance(mag_data, VectorData), 'Only VectorData objects can be mapped!'
assert mag_data.a == self.a, 'Grid spacing has to match!'
assert mag_data.dim[0] == 1, 'Magnetic distribution must be 2-dimensional!'
assert mag_data.dim[1:3] == self.dim_uv, 'Dimensions do not match!'
v_dim, u_dim = self.dim_uv
- u_mag, v_mag = mag_data.magnitude[0:2, 0, ...]
+ u_mag, v_mag = mag_data.field[0:2, 0, ...]
# Create zero padded matrices:
u_pad = int(u_dim / 2 * self.padding)
v_pad = int(v_dim / 2 * self.padding)
@@ -446,9 +443,9 @@ class PhaseMapperFDFC(PhaseMapper):
self._log.debug('Calling jac_dot')
assert len(vector) == self.n, \
'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.n)
- mag_proj = MagData(self.a, np.zeros((3, 1) + self.dim_uv, dtype=np.float32))
+ mag_proj = VectorData(self.a, np.zeros((3, 1) + self.dim_uv, dtype=np.float32))
magnitude_proj = np.reshape(vector, (2,) + self.dim_uv)
- mag_proj.magnitude[:2, 0, ...] = magnitude_proj
+ mag_proj.field[:2, 0, ...] = magnitude_proj
return self(mag_proj).phase_vec
def jac_T_dot(self, vector):
@@ -476,7 +473,7 @@ class PhaseMapperMIP(PhaseMapper):
The :class:`~.PhaseMapperMIP` class represents a phase mapping strategy for the electrostatic
contribution to the electron phase shift which results e.g. from the mean inner potential in
certain samples and which is sensitive to properties of the electron microscope. It directly
- takes :class:`~.MagData` objects and returns :class:`~.PhaseMap` objects.
+ takes :class:`~.ScalarData` objects and returns :class:`~.PhaseMap` objects.
Attributes
----------
@@ -508,7 +505,7 @@ class PhaseMapperMIP(PhaseMapper):
self.v_acc = v_acc
self.threshold = threshold
self.m = np.prod(self.dim_uv)
- self.n = np.prod(self.dim_uv)
+ self.n = self.m
# Coefficient calculation:
lam = H_BAR / np.sqrt(2 * M_E * Q_E * v_acc * (1 + Q_E * v_acc / (2 * M_E * C ** 2)))
C_e = 2 * pi * Q_E / lam * (Q_E * v_acc + M_E * C ** 2) / (
@@ -526,21 +523,14 @@ class PhaseMapperMIP(PhaseMapper):
return 'PhaseMapperMIP(a=%s, dim_uv=%s, v_0=%s, v_acc=%s, threshold=%s)' % \
(self.a, self.dim_uv, self.v_0, self.v_acc, self.threshold)
- def __call__(self, mag_data):
+ def __call__(self, elec_data):
self._log.debug('Calling __call__')
- raise NotImplementedError() # TODO: Implement right!
- # assert isinstance(mag_data, MagData), 'Only MagData objects can be mapped!'
- # assert mag_data.a == self.a, 'Grid spacing has to match!'
- # assert mag_data.dim[0] == 1, 'Magnetic distribution must be 2-dimensional!'
- # assert mag_data.dim[1:3] == self.dim_uv, 'Dimensions do not match!'
- # return self.coeff * mag_data.get_mask(self.threshold)[0, ...].reshape(self.dim_uv)
- # # Calculate mask:
- # mask = mag_data.get_mask(self.threshold)
- # # Project and calculate phase:
- # # TODO: check if projector manages scalar multiplication (problem with MagData) and fix!
- # projection = self.projector(mask.reshape(-1)).reshape(self.projector.dim_uv)
- # phase = self.coeff * projection
- # return PhaseMap(mag_data.a, phase)
+ assert isinstance(elec_data, ScalarData), 'Only ScalarData objects can be mapped!'
+ assert elec_data.a == self.a, 'Grid spacing has to match!'
+ assert elec_data.dim[0] == 1, 'Magnetic distribution must be 2-dimensional!'
+ assert elec_data.dim[1:3] == self.dim_uv, 'Dimensions do not match!'
+ phase = self.coeff * np.squeeze(elec_data.get_mask(self.threshold))
+ return PhaseMap(elec_data.a, phase)
def jac_dot(self, vector):
"""Calculate the product of the Jacobi matrix with a given `vector`.
@@ -548,9 +538,7 @@ class PhaseMapperMIP(PhaseMapper):
Parameters
----------
vector : :class:`~numpy.ndarray` (N=1)
- Vectorized form of the magnetization in `u`- and `v`-direction of every pixel
- (row-wise). The first ``N**2`` elements have to correspond to the `u`-, the next
- ``N**2`` elements to the `v`-component of the magnetization.
+ Vectorized form of the electrostatic field of every pixel (row-wise).
Returns
-------
@@ -558,7 +546,7 @@ class PhaseMapperMIP(PhaseMapper):
Product of the Jacobi matrix (which is not explicitely calculated) with the vector.
"""
- raise NotImplementedError()
+ raise NotImplementedError() # TODO: Implement right!
def jac_T_dot(self, vector):
"""Calculate the product of the transposed Jacobi matrix with a given `vector`.
@@ -573,19 +561,19 @@ class PhaseMapperMIP(PhaseMapper):
-------
result : :class:`~numpy.ndarray` (N=1)
Product of the transposed Jacobi matrix (which is not explicitely calculated) with
- the vector, which has ``2*N**2`` entries like a 2D magnetic projection.
+ the vector, which has ``N**2`` entries like an electrostatic projection.
"""
- raise NotImplementedError()
+ raise NotImplementedError() # TODO: Implement right!
def pm(mag_data, mode='z', b_0=1, **kwargs):
- """Convenience function for fast phase mapping.
+ """Convenience function for fast magnetic phase mapping.
Parameters
----------
- mag_data : :class:`~.MagData`
- A :class:`~.MagData` object, from which the projected phase map should be calculated.
+ mag_data : :class:`~.VectorData`
+ A :class:`~.VectorData` object, from which the projected phase map should be calculated.
mode: {'z', 'y', 'x', 'x-tilt', 'y-tilt', 'rot-tilt'}, optional
Projection mode which determines the :class:`~.pyramid.projector.Projector` subclass, which
is used for the projection. Default is a simple projection along the `z`-direction.
diff --git a/pyramid/projector.py b/pyramid/projector.py
index 5f0e238864d477647a0c19b9730c70e78ed4c2f0..7c6e06515b70d827c1af66b8095520063b9c8fe1 100644
--- a/pyramid/projector.py
+++ b/pyramid/projector.py
@@ -16,7 +16,7 @@ from numpy import pi
from scipy.sparse import coo_matrix, csr_matrix
import pyramid.fft as fft
-from pyramid.magdata import MagData
+from pyramid.fielddata import FieldData, VectorData, ScalarData
from pyramid.quaternion import Quaternion
__all__ = ['RotTiltProjector', 'XTiltProjector', 'YTiltProjector', 'SimpleProjector']
@@ -80,11 +80,20 @@ class Projector(object):
self._log.debug('Calling __str__')
return 'Projector(dim=%s, dim_uv=%s, coeff=%s)' % (self.dim, self.dim_uv, self.coeff)
- def __call__(self, mag_data):
- mag_proj = MagData(mag_data.a, fft.zeros((3, 1) + self.dim_uv, dtype=fft.FLOAT))
- magnitude_proj = self.jac_dot(mag_data.mag_vec).reshape((2,) + self.dim_uv)
- mag_proj.magnitude[0:2, 0, ...] = magnitude_proj
- return mag_proj
+ def __call__(self, field_data):
+ if isinstance(field_data, VectorData):
+ field_empty = fft.zeros((3, 1) + self.dim_uv, dtype=fft.FLOAT)
+ field_data_proj = VectorData(field_data.a, field_empty)
+ field_proj = self.jac_dot(field_data.field_vec).reshape((2,) + self.dim_uv)
+ field_data_proj.field[0:2, 0, ...] = field_proj
+ elif isinstance(field_data, ScalarData):
+ field_empty = fft.zeros((1,) + self.dim_uv, dtype=fft.FLOAT)
+ field_data_proj = ScalarData(field_data.a, field_empty)
+ field_proj = self.jac_dot(field_data.field_vec).reshape(self.dim_uv)
+ field_data_proj.field[0, ...] = field_proj
+ else:
+ raise TypeError('Input is neither of type VectorData or ScalarData')
+ return field_data_proj
def _vector_field_projection(self, vector):
result = fft.zeros(2 * self.size_2d, dtype=fft.FLOAT)
diff --git a/pyramid/reconstruction.py b/pyramid/reconstruction.py
index d847a70c822f3b163f71acbcdb34590d177d71ab..592cb4072a4c0a7157492315fba2e5d00f85d6e9 100644
--- a/pyramid/reconstruction.py
+++ b/pyramid/reconstruction.py
@@ -4,7 +4,7 @@
#
"""Reconstruct magnetic distributions from given phasemaps.
-This module reconstructs 3-dimensional magnetic distributions (as :class:`~pyramid.magdata.MagData`
+This module reconstructs 3-dimensional magnetic distributions (as :class:`~pyramid.magdata.VectorData`
objects) from a given set of phase maps (represented by :class:`~pyramid.phasemap.PhaseMap`
objects) by using several model based reconstruction algorithms which use the forward model
provided by :mod:`~pyramid.projector` and :mod:`~pyramid.phasemapper` and a priori knowledge of
@@ -16,7 +16,7 @@ import logging
import numpy as np
-from pyramid.magdata import MagData
+from pyramid.fielddata import VectorData
__all__ = ['optimize_linear', 'optimize_nonlin', 'optimize_splitbregman']
_log = logging.getLogger(__name__)
@@ -37,8 +37,8 @@ def optimize_linear(costfunction, max_iter=None):
Returns
-------
- mag_data : :class:`~pyramid.magdata.MagData`
- The reconstructed magnetic distribution as a :class:`~.MagData` object.
+ mag_data : :class:`~pyramid.fielddata.VectorData`
+ The reconstructed magnetic distribution as a :class:`~.VectorData` object.
"""
import jutil.cg as jcg
@@ -48,9 +48,9 @@ def optimize_linear(costfunction, max_iter=None):
_log.info('Cost after optimization: {}'.format(costfunction(x_opt)))
# Cut ramp parameters if necessary (this also saves the final parameters in the ramp class!):
x_opt = costfunction.fwd_model.ramp.extract_ramp_params(x_opt)
- # Create and return fitting MagData object:
+ # Create and return fitting VectorData object:
data_set = costfunction.fwd_model.data_set
- mag_opt = MagData(data_set.a, np.zeros((3,) + data_set.dim))
+ mag_opt = VectorData(data_set.a, np.zeros((3,) + data_set.dim))
mag_opt.set_vector(x_opt, data_set.mask)
return mag_opt
@@ -65,13 +65,13 @@ def optimize_nonlin(costfunction, first_guess=None):
costfunction : :class:`~.Costfunction`
A :class:`~.Costfunction` object which implements a specified forward model and
regularisator which is minimized in the optimization process.
- first_guess : :class:`~pyramid.magdata.MagData`
+ first_guess : :class:`~pyramid.fielddata.VectorData`
magnetization to start the non-linear iteration with.
Returns
-------
- mag_data : :class:`~pyramid.magdata.MagData`
- The reconstructed magnetic distribution as a :class:`~.MagData` object.
+ mag_data : :class:`~pyramid.fielddata.VectorData`
+ The reconstructed magnetic distribution as a :class:`~.VectorData` object.
"""
import jutil.minimizer as jmin
@@ -79,7 +79,7 @@ def optimize_nonlin(costfunction, first_guess=None):
_log.debug('Calling optimize_nonlin')
data_set = costfunction.fwd_model.data_set
if first_guess is None:
- first_guess = MagData(data_set.a, np.zeros((3,) + data_set.dim))
+ first_guess = VectorData(data_set.a, np.zeros((3,) + data_set.dim))
x_0 = first_guess.get_vector(data_set.mask)
assert len(x_0) == costfunction.n, (len(x_0), costfunction.m, costfunction.n)
@@ -102,7 +102,7 @@ def optimize_nonlin(costfunction, first_guess=None):
tol={"max_iteration": 10000})
x_opt = result.x
_log.info('Cost after optimization: {}'.format(costfunction(x_opt)))
- mag_opt = MagData(data_set.a, np.zeros((3,) + data_set.dim))
+ mag_opt = VectorData(data_set.a, np.zeros((3,) + data_set.dim))
mag_opt.set_vector(x_opt, data_set.mask)
return mag_opt
@@ -129,8 +129,8 @@ def optimize_splitbregman(costfunction, weight, lam, mu):
Returns
-------
- mag_data : :class:`~pyramid.magdata.MagData`
- The reconstructed magnetic distribution as a :class:`~.MagData` object.
+ mag_data : :class:`~pyramid.fielddata.VectorData`
+ The reconstructed magnetic distribution as a :class:`~.VectorData` object.
"""
import jutil.splitbregman as jsb
@@ -157,6 +157,6 @@ def optimize_splitbregman(costfunction, weight, lam, mu):
A, D, y,
weight=weight, mu=mu, lambd=lam, max_iter=1000)
- mag_opt = MagData(data_set.a, np.zeros((3,) + data_set.dim))
+ mag_opt = VectorData(data_set.a, np.zeros((3,) + data_set.dim))
mag_opt.set_vector(x_opt, data_set.mask)
return mag_opt
diff --git a/pyramid/tests/test_dataset.py b/pyramid/tests/test_dataset.py
index 3a3505a256672673546a0ed29dec592d4c47420f..8cb02abd8a14b1440216f7824eea59a0ad7c2422 100644
--- a/pyramid/tests/test_dataset.py
+++ b/pyramid/tests/test_dataset.py
@@ -10,7 +10,7 @@ import numpy as np
from numpy.testing import assert_allclose
from pyramid.dataset import DataSet
-from pyramid.magdata import MagData
+from pyramid.fielddata import VectorData
from pyramid.phasemap import PhaseMap
from pyramid.projector import SimpleProjector
@@ -42,7 +42,7 @@ class TestCaseDataSet(unittest.TestCase):
def test_create_phase_maps(self):
self.data.projectors = [self.projector]
- mag_data = MagData(self.a, np.ones((3,) + self.dim))
+ mag_data = VectorData(self.a, np.ones((3,) + self.dim))
self.data.phase_maps = self.data.create_phase_maps(mag_data)
phase_vec_ref = np.load(os.path.join(self.path, 'phase_vec_ref.npy'))
assert_allclose(self.data.phase_vec, phase_vec_ref, atol=1E-6,
diff --git a/pyramid/tests/test_magdata.py b/pyramid/tests/test_fielddata.py
similarity index 62%
rename from pyramid/tests/test_magdata.py
rename to pyramid/tests/test_fielddata.py
index 23691e88ef624c4a31d6b3f6b31a0601f495ecc5..f2766ad4847dcbaae9618aab103fbb950ecd2ed8 100644
--- a/pyramid/tests/test_magdata.py
+++ b/pyramid/tests/test_fielddata.py
@@ -7,15 +7,15 @@ import unittest
import numpy as np
from numpy.testing import assert_allclose
-from pyramid.magdata import MagData
+from pyramid.fielddata import VectorData
-class TestCaseMagData(unittest.TestCase):
+class TestCaseVectorData(unittest.TestCase):
def setUp(self):
- self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_magdata')
+ self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_fielddata')
magnitude = np.zeros((3, 4, 4, 4))
magnitude[:, 1:-1, 1:-1, 1:-1] = 1
- self.mag_data = MagData(10.0, magnitude)
+ self.mag_data = VectorData(10.0, magnitude)
def tearDown(self):
self.path = None
@@ -30,7 +30,7 @@ class TestCaseMagData(unittest.TestCase):
def test_scale_down(self):
self.mag_data.scale_down()
reference = 1 / 8. * np.ones((3, 2, 2, 2))
- assert_allclose(self.mag_data.magnitude, reference,
+ assert_allclose(self.mag_data.field, reference,
err_msg='Unexpected behavior in scale_down()!')
assert_allclose(self.mag_data.a, 20,
err_msg='Unexpected behavior in scale_down()!')
@@ -39,20 +39,20 @@ class TestCaseMagData(unittest.TestCase):
self.mag_data.scale_up()
reference = np.zeros((3, 8, 8, 8))
reference[:, 2:6, 2:6, 2:6] = 1
- assert_allclose(self.mag_data.magnitude, reference,
+ assert_allclose(self.mag_data.field, reference,
err_msg='Unexpected behavior in scale_down()!')
assert_allclose(self.mag_data.a, 5,
err_msg='Unexpected behavior in scale_down()!')
def test_pad(self):
- reference = self.mag_data.magnitude.copy()
+ reference = self.mag_data.field.copy()
self.mag_data.pad((1, 1, 1))
reference = np.pad(reference, ((0, 0), (1, 1), (1, 1), (1, 1)), mode='constant')
- assert_allclose(self.mag_data.magnitude, reference,
+ assert_allclose(self.mag_data.field, reference,
err_msg='Unexpected behavior in scale_down()!')
self.mag_data.pad(((1, 1), (1, 1), (1, 1)))
reference = np.pad(reference, ((0, 0), (1, 1), (1, 1), (1, 1)), mode='constant')
- assert_allclose(self.mag_data.magnitude, reference,
+ assert_allclose(self.mag_data.field, reference,
err_msg='Unexpected behavior in scale_down()!')
def test_get_mask(self):
@@ -75,48 +75,48 @@ class TestCaseMagData(unittest.TestCase):
self.mag_data.set_vector(vector, mask)
reference = np.zeros((3, 4, 4, 4))
reference[:, 1:-1, 1:-1, 1:-1] = 2
- assert_allclose(self.mag_data.magnitude, reference,
+ assert_allclose(self.mag_data.field, reference,
err_msg='Unexpected behavior in set_vector()!')
def test_flip(self):
- mag_data = MagData.load_from_hdf5(os.path.join(self.path, 'mag_data_orig.hdf5'))
- mag_data_flipx = MagData.load_from_hdf5(os.path.join(self.path, 'mag_data_flipx.hdf5'))
- mag_data_flipy = MagData.load_from_hdf5(os.path.join(self.path, 'mag_data_flipy.hdf5'))
- mag_data_flipz = MagData.load_from_hdf5(os.path.join(self.path, 'mag_data_flipz.hdf5'))
- assert_allclose(mag_data.flip('x').magnitude, mag_data_flipx.magnitude,
+ mag_data = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_data_orig.hdf5'))
+ mag_data_flipx = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_data_flipx.hdf5'))
+ mag_data_flipy = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_data_flipy.hdf5'))
+ mag_data_flipz = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_data_flipz.hdf5'))
+ assert_allclose(mag_data.flip('x').field, mag_data_flipx.field,
err_msg='Unexpected behavior in flip()! (x)')
- assert_allclose(mag_data.flip('y').magnitude, mag_data_flipy.magnitude,
+ assert_allclose(mag_data.flip('y').field, mag_data_flipy.field,
err_msg='Unexpected behavior in flip()! (y)')
- assert_allclose(mag_data.flip('z').magnitude, mag_data_flipz.magnitude,
+ assert_allclose(mag_data.flip('z').field, mag_data_flipz.field,
err_msg='Unexpected behavior in flip()! (z)')
def test_rot(self):
- mag_data = MagData.load_from_hdf5(os.path.join(self.path, 'mag_data_orig.hdf5'))
- mag_data_rotx = MagData.load_from_hdf5(os.path.join(self.path, 'mag_data_rotx.hdf5'))
- mag_data_roty = MagData.load_from_hdf5(os.path.join(self.path, 'mag_data_roty.hdf5'))
- mag_data_rotz = MagData.load_from_hdf5(os.path.join(self.path, 'mag_data_rotz.hdf5'))
- assert_allclose(mag_data.rot90('x').magnitude, mag_data_rotx.magnitude,
+ mag_data = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_data_orig.hdf5'))
+ mag_data_rotx = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_data_rotx.hdf5'))
+ mag_data_roty = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_data_roty.hdf5'))
+ mag_data_rotz = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_data_rotz.hdf5'))
+ assert_allclose(mag_data.rot90('x').field, mag_data_rotx.field,
err_msg='Unexpected behavior in rot()! (x)')
- assert_allclose(mag_data.rot90('y').magnitude, mag_data_roty.magnitude,
+ assert_allclose(mag_data.rot90('y').field, mag_data_roty.field,
err_msg='Unexpected behavior in rot()! (y)')
- assert_allclose(mag_data.rot90('z').magnitude, mag_data_rotz.magnitude,
+ assert_allclose(mag_data.rot90('z').field, mag_data_rotz.field,
err_msg='Unexpected behavior in rot()! (z)')
def test_load_from_llg(self):
- mag_data = MagData.load_from_llg(os.path.join(self.path, 'mag_data_ref_load.txt'))
- assert_allclose(mag_data.magnitude, self.mag_data.magnitude,
+ mag_data = VectorData.load_from_llg(os.path.join(self.path, 'mag_data_ref_load.txt'))
+ assert_allclose(mag_data.field, self.mag_data.field,
err_msg='Unexpected behavior in load_from_llg()!')
assert_allclose(mag_data.a, self.mag_data.a,
err_msg='Unexpected behavior in load_from_llg()!')
def test_load_from_hdf5(self):
- mag_data = MagData.load_from_hdf5(os.path.join(self.path, 'mag_data_ref_load.hdf5'))
- assert_allclose(mag_data.magnitude, self.mag_data.magnitude,
+ mag_data = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_data_ref_load.hdf5'))
+ assert_allclose(mag_data.field, self.mag_data.field,
err_msg='Unexpected behavior in load_from_netcdf4()!')
assert_allclose(mag_data.a, self.mag_data.a,
err_msg='Unexpected behavior in load_from_netcdf4()!')
if __name__ == '__main__':
- suite = unittest.TestLoader().loadTestsFromTestCase(TestCaseMagData)
+ suite = unittest.TestLoader().loadTestsFromTestCase(TestCaseVectorData)
unittest.TextTestRunner(verbosity=2).run(suite)
diff --git a/pyramid/tests/test_magdata/mag_data_flipx.hdf5 b/pyramid/tests/test_fielddata/mag_data_flipx.hdf5
similarity index 100%
rename from pyramid/tests/test_magdata/mag_data_flipx.hdf5
rename to pyramid/tests/test_fielddata/mag_data_flipx.hdf5
diff --git a/pyramid/tests/test_magdata/mag_data_flipy.hdf5 b/pyramid/tests/test_fielddata/mag_data_flipy.hdf5
similarity index 100%
rename from pyramid/tests/test_magdata/mag_data_flipy.hdf5
rename to pyramid/tests/test_fielddata/mag_data_flipy.hdf5
diff --git a/pyramid/tests/test_magdata/mag_data_flipz.hdf5 b/pyramid/tests/test_fielddata/mag_data_flipz.hdf5
similarity index 100%
rename from pyramid/tests/test_magdata/mag_data_flipz.hdf5
rename to pyramid/tests/test_fielddata/mag_data_flipz.hdf5
diff --git a/pyramid/tests/test_magdata/mag_data_orig.hdf5 b/pyramid/tests/test_fielddata/mag_data_orig.hdf5
similarity index 100%
rename from pyramid/tests/test_magdata/mag_data_orig.hdf5
rename to pyramid/tests/test_fielddata/mag_data_orig.hdf5
diff --git a/pyramid/tests/test_magdata/mag_data_ref_load.hdf5 b/pyramid/tests/test_fielddata/mag_data_ref_load.hdf5
similarity index 100%
rename from pyramid/tests/test_magdata/mag_data_ref_load.hdf5
rename to pyramid/tests/test_fielddata/mag_data_ref_load.hdf5
diff --git a/pyramid/tests/test_magdata/mag_data_ref_load.txt b/pyramid/tests/test_fielddata/mag_data_ref_load.txt
similarity index 100%
rename from pyramid/tests/test_magdata/mag_data_ref_load.txt
rename to pyramid/tests/test_fielddata/mag_data_ref_load.txt
diff --git a/pyramid/tests/test_magdata/mag_data_rotx.hdf5 b/pyramid/tests/test_fielddata/mag_data_rotx.hdf5
similarity index 100%
rename from pyramid/tests/test_magdata/mag_data_rotx.hdf5
rename to pyramid/tests/test_fielddata/mag_data_rotx.hdf5
diff --git a/pyramid/tests/test_magdata/mag_data_roty.hdf5 b/pyramid/tests/test_fielddata/mag_data_roty.hdf5
similarity index 100%
rename from pyramid/tests/test_magdata/mag_data_roty.hdf5
rename to pyramid/tests/test_fielddata/mag_data_roty.hdf5
diff --git a/pyramid/tests/test_magdata/mag_data_rotz.hdf5 b/pyramid/tests/test_fielddata/mag_data_rotz.hdf5
similarity index 100%
rename from pyramid/tests/test_magdata/mag_data_rotz.hdf5
rename to pyramid/tests/test_fielddata/mag_data_rotz.hdf5
diff --git a/pyramid/tests/test_phasemapper.py b/pyramid/tests/test_phasemapper.py
index 1b9f5fee9a6db16a12f7e890f24b1a77147952e0..d743f2c344c986df3e6ef7c4ea92f5c10bec1f42 100644
--- a/pyramid/tests/test_phasemapper.py
+++ b/pyramid/tests/test_phasemapper.py
@@ -8,16 +8,16 @@ import numpy as np
from numpy.testing import assert_allclose
from pyramid.kernel import Kernel
-from pyramid.magdata import MagData
+from pyramid.fielddata import VectorData, ScalarData
from pyramid.phasemap import PhaseMap
-from pyramid.phasemapper import PhaseMapperMIP, pm
from pyramid.phasemapper import PhaseMapperRDFC, PhaseMapperRDRC, PhaseMapperFDFC
+from pyramid.phasemapper import PhaseMapperMIP, pm
class TestCasePhaseMapperRDFC(unittest.TestCase):
def setUp(self):
self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
- self.mag_proj = MagData.load_from_hdf5(os.path.join(self.path, 'mag_proj.hdf5'))
+ self.mag_proj = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_proj.hdf5'))
self.mapper = PhaseMapperRDFC(Kernel(self.mag_proj.a, self.mag_proj.dim[1:]))
def tearDown(self):
@@ -34,7 +34,7 @@ class TestCasePhaseMapperRDFC(unittest.TestCase):
def test_PhaseMapperRDFC_jac_dot(self):
phase = self.mapper(self.mag_proj).phase
- mag_proj_vec = self.mag_proj.magnitude[:2, ...].flatten()
+ mag_proj_vec = self.mag_proj.field[:2, ...].flatten()
phase_jac = self.mapper.jac_dot(mag_proj_vec).reshape(self.mapper.kernel.dim_uv)
assert_allclose(phase, phase_jac, atol=1E-7,
err_msg='Inconsistency between __call__() and jac_dot()!')
@@ -55,7 +55,7 @@ class TestCasePhaseMapperRDFC(unittest.TestCase):
class TestCasePhaseMapperRDRC(unittest.TestCase):
def setUp(self):
self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
- self.mag_proj = MagData.load_from_hdf5(os.path.join(self.path, 'mag_proj.hdf5'))
+ self.mag_proj = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_proj.hdf5'))
self.mapper = PhaseMapperRDRC(Kernel(self.mag_proj.a, self.mag_proj.dim[1:]))
def tearDown(self):
@@ -72,7 +72,7 @@ class TestCasePhaseMapperRDRC(unittest.TestCase):
def test_PhaseMapperRDRC_jac_dot(self):
phase = self.mapper(self.mag_proj).phase
- mag_proj_vec = self.mag_proj.magnitude[:2, ...].flatten()
+ mag_proj_vec = self.mag_proj.field[:2, ...].flatten()
phase_jac = self.mapper.jac_dot(mag_proj_vec).reshape(self.mapper.kernel.dim_uv)
assert_allclose(phase, phase_jac, atol=1E-7,
err_msg='Inconsistency between __call__() and jac_dot()!')
@@ -93,7 +93,7 @@ class TestCasePhaseMapperRDRC(unittest.TestCase):
class TestCasePhaseMapperFDFC(unittest.TestCase):
def setUp(self):
self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
- self.mag_proj = MagData.load_from_hdf5(os.path.join(self.path, 'mag_proj.hdf5'))
+ self.mag_proj = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_proj.hdf5'))
self.mapper = PhaseMapperFDFC(self.mag_proj.a, self.mag_proj.dim[1:], padding=0)
def tearDown(self):
@@ -110,7 +110,7 @@ class TestCasePhaseMapperFDFC(unittest.TestCase):
def test_PhaseMapperFDFC_jac_dot(self):
phase = self.mapper(self.mag_proj).phase
- mag_proj_vec = self.mag_proj.magnitude[:2, ...].flatten()
+ mag_proj_vec = self.mag_proj.field[:2, ...].flatten()
phase_jac = self.mapper.jac_dot(mag_proj_vec).reshape(self.mapper.dim_uv)
assert_allclose(phase, phase_jac, atol=1E-7,
err_msg='Inconsistency between __call__() and jac_dot()!')
@@ -124,10 +124,10 @@ class TestCasePhaseMapperFDFC(unittest.TestCase):
self.assertRaises(NotImplementedError, self.mapper.jac_T_dot, None)
-class TestCasePhaseMapperElectric(unittest.TestCase):
+class TestCasePhaseMapperMIP(unittest.TestCase):
def setUp(self):
self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
- self.mag_proj = MagData.load_from_hdf5(os.path.join(self.path, 'mag_proj.hdf5'))
+ self.mag_proj = ScalarData.load_from_hdf5(os.path.join(self.path, 'elec_proj.hdf5'))
self.mapper = PhaseMapperMIP(self.mag_proj.a, self.mag_proj.dim[1:])
def tearDown(self):
@@ -136,7 +136,11 @@ class TestCasePhaseMapperElectric(unittest.TestCase):
self.mapper = None
def test_call(self):
- self.assertRaises(NotImplementedError, self.mapper, None)
+ phase_ref = PhaseMap.load_from_hdf5(os.path.join(self.path, 'phase_map_elec.hdf5'))
+ phase_map = self.mapper(self.mag_proj)
+ assert_allclose(phase_map.phase, phase_ref.phase, atol=1E-7,
+ err_msg='Unexpected behavior in __call__()!')
+ assert_allclose(phase_map.a, phase_ref.a, err_msg='Unexpected behavior in __call__()!')
def test_jac_dot(self):
self.assertRaises(NotImplementedError, self.mapper.jac_dot, None)
@@ -148,7 +152,7 @@ class TestCasePhaseMapperElectric(unittest.TestCase):
class TestCasePM(unittest.TestCase):
def setUp(self):
self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
- self.mag_proj = MagData.load_from_hdf5(os.path.join(self.path, 'mag_proj.hdf5'))
+ self.mag_proj = VectorData.load_from_hdf5(os.path.join(self.path, 'mag_proj.hdf5'))
def tearDown(self):
self.path = None
@@ -170,7 +174,7 @@ if __name__ == '__main__':
unittest.TextTestRunner(verbosity=2).run(suite)
suite = unittest.TestLoader().loadTestsFromTestCase(TestCasePhaseMapperFDFC)
unittest.TextTestRunner(verbosity=2).run(suite)
- suite = unittest.TestLoader().loadTestsFromTestCase(TestCasePhaseMapperElectric)
+ suite = unittest.TestLoader().loadTestsFromTestCase(TestCasePhaseMapperMIP)
unittest.TextTestRunner(verbosity=2).run(suite)
suite = unittest.TestLoader().loadTestsFromTestCase(TestCasePM)
unittest.TextTestRunner(verbosity=2).run(suite)
diff --git a/pyramid/tests/test_phasemapper/elec_proj.hdf5 b/pyramid/tests/test_phasemapper/elec_proj.hdf5
new file mode 100644
index 0000000000000000000000000000000000000000..0a8c792bcc15d81ca923d4577cf2cad6d8600839
Binary files /dev/null and b/pyramid/tests/test_phasemapper/elec_proj.hdf5 differ
diff --git a/pyramid/tests/test_phasemapper/phase_map_elec.hdf5 b/pyramid/tests/test_phasemapper/phase_map_elec.hdf5
new file mode 100644
index 0000000000000000000000000000000000000000..140749420e420631d6bf2883a3df619ed9f42b94
Binary files /dev/null and b/pyramid/tests/test_phasemapper/phase_map_elec.hdf5 differ
diff --git a/pyramid/tests/test_phasemapper/ref_phase_elec.npy b/pyramid/tests/test_phasemapper/ref_phase_elec.npy
deleted file mode 100644
index 506b4882208d1e413818aea5126d865a9782603a..0000000000000000000000000000000000000000
Binary files a/pyramid/tests/test_phasemapper/ref_phase_elec.npy and /dev/null differ
diff --git a/pyramid/tests/test_phasemapper/ref_phase_mag_disc.npy b/pyramid/tests/test_phasemapper/ref_phase_mag_disc.npy
deleted file mode 100644
index 32a53e451d64445777a84bdfc3f42a92190a497f..0000000000000000000000000000000000000000
Binary files a/pyramid/tests/test_phasemapper/ref_phase_mag_disc.npy and /dev/null differ
diff --git a/pyramid/tests/test_phasemapper/ref_phase_mag_fft.npy b/pyramid/tests/test_phasemapper/ref_phase_mag_fft.npy
deleted file mode 100644
index ce42b12c1c4fb8bf294d5a850e9a69a42dcda827..0000000000000000000000000000000000000000
Binary files a/pyramid/tests/test_phasemapper/ref_phase_mag_fft.npy and /dev/null differ
diff --git a/pyramid/tests/test_phasemapper/ref_phase_mag_slab.npy b/pyramid/tests/test_phasemapper/ref_phase_mag_slab.npy
deleted file mode 100644
index 1c761d58d307a7190094092a94712d9d67abd4fe..0000000000000000000000000000000000000000
Binary files a/pyramid/tests/test_phasemapper/ref_phase_mag_slab.npy and /dev/null differ
diff --git a/pyramid/tests/test_projector.py b/pyramid/tests/test_projector.py
index 7463afde2aaddff2d3e2aa19ad2aa8452954aa77..f3498d6a798ac128fcbf42d0a2344aea5afca83c 100644
--- a/pyramid/tests/test_projector.py
+++ b/pyramid/tests/test_projector.py
@@ -8,14 +8,14 @@ import numpy as np
from numpy import pi
from numpy.testing import assert_allclose
-from pyramid.magdata import MagData
+from pyramid.fielddata import VectorData
from pyramid.projector import XTiltProjector, YTiltProjector, SimpleProjector
class TestCaseSimpleProjector(unittest.TestCase):
def setUp(self):
self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_projector')
- self.mag_data = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_data.hdf5'))
+ self.mag_data = VectorData.load_from_hdf5(os.path.join(self.path, 'ref_mag_data.hdf5'))
self.proj_z = SimpleProjector(self.mag_data.dim, axis='z')
self.proj_y = SimpleProjector(self.mag_data.dim, axis='y')
self.proj_x = SimpleProjector(self.mag_data.dim, axis='x')
@@ -31,29 +31,29 @@ class TestCaseSimpleProjector(unittest.TestCase):
mag_proj_z = self.proj_z(self.mag_data)
mag_proj_y = self.proj_y(self.mag_data)
mag_proj_x = self.proj_x(self.mag_data)
- mag_proj_z_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_z.hdf5'))
- mag_proj_y_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_y.hdf5'))
- mag_proj_x_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_x.hdf5'))
- assert_allclose(mag_proj_z.magnitude, mag_proj_z_ref.magnitude,
+ mag_proj_z_ref = VectorData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_z.hdf5'))
+ mag_proj_y_ref = VectorData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_y.hdf5'))
+ mag_proj_x_ref = VectorData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_x.hdf5'))
+ assert_allclose(mag_proj_z.field, mag_proj_z_ref.field,
err_msg='Unexpected behaviour in SimpleProjector (z-axis)')
- assert_allclose(mag_proj_y.magnitude, mag_proj_y_ref.magnitude,
+ assert_allclose(mag_proj_y.field, mag_proj_y_ref.field,
err_msg='Unexpected behaviour in SimpleProjector (y-axis)')
- assert_allclose(mag_proj_x.magnitude, mag_proj_x_ref.magnitude,
+ assert_allclose(mag_proj_x.field, mag_proj_x_ref.field,
err_msg='Unexpected behaviour in SimpleProjector (x-axis)')
def test_SimpleProjector_jac_dot(self):
- mag_vec = self.mag_data.mag_vec
+ mag_vec = self.mag_data.field_vec
mag_proj_z = self.proj_z.jac_dot(mag_vec).reshape((2,) + self.proj_z.dim_uv)
mag_proj_y = self.proj_y.jac_dot(mag_vec).reshape((2,) + self.proj_y.dim_uv)
mag_proj_x = self.proj_x.jac_dot(mag_vec).reshape((2,) + self.proj_x.dim_uv)
- mag_proj_z_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_z.hdf5'))
- mag_proj_y_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_y.hdf5'))
- mag_proj_x_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_x.hdf5'))
- assert_allclose(mag_proj_z, mag_proj_z_ref.magnitude[:2, 0, ...],
+ mag_proj_z_ref = VectorData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_z.hdf5'))
+ mag_proj_y_ref = VectorData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_y.hdf5'))
+ mag_proj_x_ref = VectorData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_x.hdf5'))
+ assert_allclose(mag_proj_z, mag_proj_z_ref.field[:2, 0, ...],
err_msg='Inconsistency between __call__() and jac_dot()! (z-axis)')
- assert_allclose(mag_proj_y, mag_proj_y_ref.magnitude[:2, 0, ...],
+ assert_allclose(mag_proj_y, mag_proj_y_ref.field[:2, 0, ...],
err_msg='Inconsistency between __call__() and jac_dot()! (y-axis)')
- assert_allclose(mag_proj_x, mag_proj_x_ref.magnitude[:2, 0, ...],
+ assert_allclose(mag_proj_x, mag_proj_x_ref.field[:2, 0, ...],
err_msg='Inconsistency between __call__() and jac_dot()! (x-axis)')
nz = self.proj_z.n
ny = self.proj_y.n
@@ -92,7 +92,7 @@ class TestCaseSimpleProjector(unittest.TestCase):
class TestCaseXTiltProjector(unittest.TestCase):
def setUp(self):
self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_projector')
- self.mag_data = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_data.hdf5'))
+ self.mag_data = VectorData.load_from_hdf5(os.path.join(self.path, 'ref_mag_data.hdf5'))
self.proj_00 = XTiltProjector(self.mag_data.dim, tilt=0)
self.proj_45 = XTiltProjector(self.mag_data.dim, tilt=pi / 4)
self.proj_90 = XTiltProjector(self.mag_data.dim, tilt=pi / 2)
@@ -108,29 +108,35 @@ class TestCaseXTiltProjector(unittest.TestCase):
mag_proj_00 = self.proj_00(self.mag_data)
mag_proj_45 = self.proj_45(self.mag_data)
mag_proj_90 = self.proj_90(self.mag_data)
- mag_proj_00_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_x00.hdf5'))
- mag_proj_45_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_x45.hdf5'))
- mag_proj_90_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_x90.hdf5'))
- assert_allclose(mag_proj_00.magnitude, mag_proj_00_ref.magnitude,
+ mag_proj_00_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_x00.hdf5'))
+ mag_proj_45_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_x45.hdf5'))
+ mag_proj_90_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_x90.hdf5'))
+ assert_allclose(mag_proj_00.field, mag_proj_00_ref.field,
err_msg='Unexpected behaviour in XTiltProjector (0°)')
- assert_allclose(mag_proj_45.magnitude, mag_proj_45_ref.magnitude,
+ assert_allclose(mag_proj_45.field, mag_proj_45_ref.field,
err_msg='Unexpected behaviour in XTiltProjector (45°)')
- assert_allclose(mag_proj_90.magnitude, mag_proj_90_ref.magnitude,
+ assert_allclose(mag_proj_90.field, mag_proj_90_ref.field,
err_msg='Unexpected behaviour in XTiltProjector (90°)')
def test_XTiltProjector_jac_dot(self):
- mag_vec = self.mag_data.mag_vec
+ mag_vec = self.mag_data.field_vec
mag_proj_00 = self.proj_00.jac_dot(mag_vec).reshape((2,) + self.proj_00.dim_uv)
mag_proj_45 = self.proj_45.jac_dot(mag_vec).reshape((2,) + self.proj_45.dim_uv)
mag_proj_90 = self.proj_90.jac_dot(mag_vec).reshape((2,) + self.proj_90.dim_uv)
- mag_proj_00_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_x00.hdf5'))
- mag_proj_45_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_x45.hdf5'))
- mag_proj_90_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_x90.hdf5'))
- assert_allclose(mag_proj_00, mag_proj_00_ref.magnitude[:2, 0, ...],
+ mag_proj_00_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_x00.hdf5'))
+ mag_proj_45_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_x45.hdf5'))
+ mag_proj_90_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_x90.hdf5'))
+ assert_allclose(mag_proj_00, mag_proj_00_ref.field[:2, 0, ...],
err_msg='Inconsistency between __call__() and jac_dot()! (0°)')
- assert_allclose(mag_proj_45, mag_proj_45_ref.magnitude[:2, 0, ...],
+ assert_allclose(mag_proj_45, mag_proj_45_ref.field[:2, 0, ...],
err_msg='Inconsistency between __call__() and jac_dot()! (45°)')
- assert_allclose(mag_proj_90, mag_proj_90_ref.magnitude[:2, 0, ...],
+ assert_allclose(mag_proj_90, mag_proj_90_ref.field[:2, 0, ...],
err_msg='Inconsistency between __call__() and jac_dot()! (90°)')
n00 = self.proj_00.n
n45 = self.proj_45.n
@@ -169,7 +175,7 @@ class TestCaseXTiltProjector(unittest.TestCase):
class TestCaseYTiltProjector(unittest.TestCase):
def setUp(self):
self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_projector')
- self.mag_data = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_data.hdf5'))
+ self.mag_data = VectorData.load_from_hdf5(os.path.join(self.path, 'ref_mag_data.hdf5'))
self.proj_00 = YTiltProjector(self.mag_data.dim, tilt=0)
self.proj_45 = YTiltProjector(self.mag_data.dim, tilt=pi / 4)
self.proj_90 = YTiltProjector(self.mag_data.dim, tilt=pi / 2)
@@ -185,29 +191,35 @@ class TestCaseYTiltProjector(unittest.TestCase):
mag_proj_00 = self.proj_00(self.mag_data)
mag_proj_45 = self.proj_45(self.mag_data)
mag_proj_90 = self.proj_90(self.mag_data)
- mag_proj_00_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_y00.hdf5'))
- mag_proj_45_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_y45.hdf5'))
- mag_proj_90_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_y90.hdf5'))
- assert_allclose(mag_proj_00.magnitude, mag_proj_00_ref.magnitude,
+ mag_proj_00_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_y00.hdf5'))
+ mag_proj_45_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_y45.hdf5'))
+ mag_proj_90_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_y90.hdf5'))
+ assert_allclose(mag_proj_00.field, mag_proj_00_ref.field,
err_msg='Unexpected behaviour in XTiltProjector (0°)')
- assert_allclose(mag_proj_45.magnitude, mag_proj_45_ref.magnitude,
+ assert_allclose(mag_proj_45.field, mag_proj_45_ref.field,
err_msg='Unexpected behaviour in XTiltProjector (45°)')
- assert_allclose(mag_proj_90.magnitude, mag_proj_90_ref.magnitude,
+ assert_allclose(mag_proj_90.field, mag_proj_90_ref.field,
err_msg='Unexpected behaviour in XTiltProjector (90°)')
def test_XTiltProjector_jac_dot(self):
- mag_vec = self.mag_data.mag_vec
+ mag_vec = self.mag_data.field_vec
mag_proj_00 = self.proj_00.jac_dot(mag_vec).reshape((2,) + self.proj_00.dim_uv)
mag_proj_45 = self.proj_45.jac_dot(mag_vec).reshape((2,) + self.proj_45.dim_uv)
mag_proj_90 = self.proj_90.jac_dot(mag_vec).reshape((2,) + self.proj_90.dim_uv)
- mag_proj_00_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_y00.hdf5'))
- mag_proj_45_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_y45.hdf5'))
- mag_proj_90_ref = MagData.load_from_hdf5(os.path.join(self.path, 'ref_mag_proj_y90.hdf5'))
- assert_allclose(mag_proj_00, mag_proj_00_ref.magnitude[:2, 0, ...],
+ mag_proj_00_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_y00.hdf5'))
+ mag_proj_45_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_y45.hdf5'))
+ mag_proj_90_ref = VectorData.load_from_hdf5(
+ os.path.join(self.path, 'ref_mag_proj_y90.hdf5'))
+ assert_allclose(mag_proj_00, mag_proj_00_ref.field[:2, 0, ...],
err_msg='Inconsistency between __call__() and jac_dot()! (0°)')
- assert_allclose(mag_proj_45, mag_proj_45_ref.magnitude[:2, 0, ...],
+ assert_allclose(mag_proj_45, mag_proj_45_ref.field[:2, 0, ...],
err_msg='Inconsistency between __call__() and jac_dot()! (45°)')
- assert_allclose(mag_proj_90, mag_proj_90_ref.magnitude[:2, 0, ...],
+ assert_allclose(mag_proj_90, mag_proj_90_ref.field[:2, 0, ...],
err_msg='Inconsistency between __call__() and jac_dot()! (90°)')
n00 = self.proj_00.n
n45 = self.proj_45.n
diff --git a/scripts/gui/mag_slicer.py b/scripts/gui/mag_slicer.py
index 91819100dbe79185e5bfcc5f3a89a50ad0ae38ff..52a1503630a04ab0784b016b59491e4476838798 100644
--- a/scripts/gui/mag_slicer.py
+++ b/scripts/gui/mag_slicer.py
@@ -13,7 +13,7 @@ import sys
import pyramid
from pyramid.kernel import Kernel
-from pyramid.magdata import MagData
+from pyramid.fielddata import VectorData
from pyramid.phasemapper import PhaseMapperRDFC
from pyramid.projector import SimpleProjector
@@ -231,7 +231,7 @@ class UI_MagSlicerMain(QtGui.QWidget):
directory = os.path.join(pyramid.DIR_FILES, 'magdata')
mag_file = QtGui.QFileDialog.getOpenFileName(self, 'Open Data File', directory,
'HDF5 files (*.hdf5)')
- self.mag_data = MagData.load_from_hdf5(mag_file)
+ self.mag_data = VectorData.load_from_hdf5(mag_file)
self.mag_data_loaded = True
self.mplWidgetMag.axes.set_visible(True)
self.mplWidgetHolo.axes.set_visible(True)
diff --git a/scripts/magdata/magcreator/create_alternating_filaments.py b/scripts/magdata/magcreator/create_alternating_filaments.py
index a59afa2f873945f59a13607303e414fd9e4650bf..60a906849747f6b14039ad263823f81963570d0f 100644
--- a/scripts/magdata/magcreator/create_alternating_filaments.py
+++ b/scripts/magdata/magcreator/create_alternating_filaments.py
@@ -19,12 +19,12 @@ magnitude = 1
spacing = 5
filename = 'magdata_mc_alternating_filaments_spacing={}.nc'.format(spacing)
-# Create and save MagData object:
-mag_data = py.MagData(a, np.zeros((3,)+dim))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, np.zeros((3,) + dim))
count = int((dim[1]-1) / spacing) + 1
for i in range(count):
pos = i * spacing
mag_shape = py.magcreator.Shapes.filament(dim, (0, pos))
- mag_data += py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi))
+ mag_data += py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi))
phi *= -1 # Switch the angle
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_array_sphere_disc_slab.py b/scripts/magdata/magcreator/create_array_sphere_disc_slab.py
index e324947fb8e58b8ed938de9ead27d0492467865e..18d71e401dd9b2fda46d4dc6cf69e881a87dd5cc 100644
--- a/scripts/magdata/magcreator/create_array_sphere_disc_slab.py
+++ b/scripts/magdata/magcreator/create_array_sphere_disc_slab.py
@@ -29,8 +29,8 @@ center = (32, 96, 64) # in px (z, y, x), index starts with 0!
radius = 24 # in px
mag_shape_sphere = py.magcreator.Shapes.sphere(dim, center, radius)
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape_slab, np.pi/4))
-mag_data += py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape_disc, np.pi/2))
-mag_data += py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape_sphere, np.pi))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape_slab, np.pi / 4))
+mag_data += py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape_disc, np.pi / 2))
+mag_data += py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape_sphere, np.pi))
mag_data.save_to_hdf5(filename)
diff --git a/scripts/magdata/magcreator/create_core_shell_disc.py b/scripts/magdata/magcreator/create_core_shell_disc.py
index 87310b8a6976ed6a0a143a94b1131cc9cc014d57..b28c4bfb86f109f0fb608542751047ec87c3f395 100644
--- a/scripts/magdata/magcreator/create_core_shell_disc.py
+++ b/scripts/magdata/magcreator/create_core_shell_disc.py
@@ -24,7 +24,7 @@ mag_shape_core = py.magcreator.Shapes.disc(dim, center, radius_core, height)
mag_shape_outer = py.magcreator.Shapes.disc(dim, center, radius_shell, height)
mag_shape_shell = np.logical_xor(mag_shape_outer, mag_shape_core)
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_vortex(mag_shape_shell, magnitude=0.75))
-mag_data += py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape_core, phi=0, theta=0))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, py.magcreator.create_mag_dist_vortex(mag_shape_shell, amplitude=0.75))
+mag_data += py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape_core, phi=0, theta=0))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_core_shell_sphere.py b/scripts/magdata/magcreator/create_core_shell_sphere.py
index 06e22065a5a6615412f074b5683aa68dc5d5971b..64b3dea2683b0ea33c81e8660aeb1b49173b9bd0 100644
--- a/scripts/magdata/magcreator/create_core_shell_sphere.py
+++ b/scripts/magdata/magcreator/create_core_shell_sphere.py
@@ -24,7 +24,7 @@ mag_shape_disc = py.magcreator.Shapes.disc(dim, center, radius_core, height=dim[
mag_shape_core = np.logical_and(mag_shape_sphere, mag_shape_disc)
mag_shape_shell = np.logical_and(mag_shape_sphere, np.logical_not(mag_shape_core))
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_vortex(mag_shape_shell, magnitude=0.75))
-mag_data += py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape_core, phi=0, theta=0))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, py.magcreator.create_mag_dist_vortex(mag_shape_shell, amplitude=0.75))
+mag_data += py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape_core, phi=0, theta=0))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_homog_disc.py b/scripts/magdata/magcreator/create_homog_disc.py
index 2ca2f84154b20e22bec406472ff0edcafe36e952..d3f2c284b0456897fea489e5e191f1b517777333 100644
--- a/scripts/magdata/magcreator/create_homog_disc.py
+++ b/scripts/magdata/magcreator/create_homog_disc.py
@@ -24,6 +24,6 @@ radius = dim[2]//4
height = dim[0]//2
mag_shape = py.magcreator.Shapes.disc(dim, center, radius, height)
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_homog_filament.py b/scripts/magdata/magcreator/create_homog_filament.py
index fe036c607dc77bef46832b89421f82ffc99da551..3ac6eb7a159d3bec735a8eccb1afe1847a5b06be 100644
--- a/scripts/magdata/magcreator/create_homog_filament.py
+++ b/scripts/magdata/magcreator/create_homog_filament.py
@@ -22,6 +22,6 @@ filename = 'magdata_mc_homog_filament.nc'
pos = (0, dim[1]//2)
mag_shape = py.magcreator.Shapes.filament(dim, pos)
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_homog_pixel.py b/scripts/magdata/magcreator/create_homog_pixel.py
index d2358a38d79dc3cab769aabd9e8ae8e94a94f2d2..8dd222f03708164d9680899173e4ce0583963ca0 100644
--- a/scripts/magdata/magcreator/create_homog_pixel.py
+++ b/scripts/magdata/magcreator/create_homog_pixel.py
@@ -22,6 +22,6 @@ filename = 'magdata_mc_pixel.nc'
pixel = (0, dim[1]//4, dim[2]//4)
mag_shape = py.magcreator.Shapes.pixel(dim, pixel)
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_homog_slab.py b/scripts/magdata/magcreator/create_homog_slab.py
index 5d1394cf9314dae03a345c4d52a4a11587da6e8e..80008b81d79411ce8250acf1573afa025af4df0b 100644
--- a/scripts/magdata/magcreator/create_homog_slab.py
+++ b/scripts/magdata/magcreator/create_homog_slab.py
@@ -23,6 +23,6 @@ center = (dim[0]//2-0.5, dim[1]//2-0.5, dim[2]//2-0.5)
width = (dim[0]//8, dim[1]//2, dim[2]//4)
mag_shape = py.magcreator.Shapes.slab(dim, center, width)
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_homog_sphere.py b/scripts/magdata/magcreator/create_homog_sphere.py
index 244e203aa83f00511939c72d958759d5f7f2ccfe..0fd1c7572adda87d8eddf51461504ecfae5c0e59 100644
--- a/scripts/magdata/magcreator/create_homog_sphere.py
+++ b/scripts/magdata/magcreator/create_homog_sphere.py
@@ -23,6 +23,6 @@ center = (dim[0]//2-0.5, dim[1]//2-0.5, dim[2]//2-0.5)
radius = dim[2]//4 # in px
mag_shape = py.magcreator.Shapes.sphere(dim, center, radius)
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_paper2_homog_slab.py b/scripts/magdata/magcreator/create_paper2_homog_slab.py
index 33a0e735c0ba6e98ad6a7148a647548ef33b286f..35deeca5c6f53b933b2e712a41ad21e6e7018bfc 100644
--- a/scripts/magdata/magcreator/create_paper2_homog_slab.py
+++ b/scripts/magdata/magcreator/create_paper2_homog_slab.py
@@ -26,10 +26,10 @@ width = (0, 80, 80) # in px
mag_shape_1 = py.magcreator.Shapes.slab(dim, center_1, width)
mag_shape_2 = py.magcreator.Shapes.slab(dim, center_2, width)
-# Create and save MagData object:
-mag = py.magcreator.create_mag_dist_homog(mag_shape_1, phi=7/12.*np.pi, magnitude=magnitude)
-mag += py.magcreator.create_mag_dist_homog(mag_shape_2, phi=1/3.*np.pi, magnitude=magnitude)
-mag_data = py.MagData(a, mag)
+# Create and save VectorData object:
+mag = py.magcreator.create_mag_dist_homog(mag_shape_1, phi=7 / 12. * np.pi, amplitude=magnitude)
+mag += py.magcreator.create_mag_dist_homog(mag_shape_2, phi=1 / 3. * np.pi, amplitude=magnitude)
+mag_data = py.VectorData(a, mag)
projector = py.RotTiltProjector(mag_data.dim, rotation, tilt)
mag_data = projector(mag_data)
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_paper2_vortex_slab.py b/scripts/magdata/magcreator/create_paper2_vortex_slab.py
index a3ff61445ffa3a08299ef3a2577a6948d4f93c49..f7574e55d54542631a96d657c4cc1b2817dba8de 100644
--- a/scripts/magdata/magcreator/create_paper2_vortex_slab.py
+++ b/scripts/magdata/magcreator/create_paper2_vortex_slab.py
@@ -21,6 +21,7 @@ center = (0, dim[1]//2-0.5, dim[2]//2-0.5)
width = (0, 128, 128) # in px
mag_shape = py.magcreator.Shapes.slab(dim, center, width)
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_vortex(mag_shape, center, axis, magnitude))
+# Create and save VectorData object:
+mag_data = py.VectorData(a,
+ py.magcreator.create_mag_dist_vortex(mag_shape, center, axis, magnitude))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_pyramid_logo.py b/scripts/magdata/magcreator/create_pyramid_logo.py
index b399924786874a3093d55bf0c83bb434e428efc6..55b6c7c4d147da0959e324d55d359158ff9bd512 100644
--- a/scripts/magdata/magcreator/create_pyramid_logo.py
+++ b/scripts/magdata/magcreator/create_pyramid_logo.py
@@ -28,6 +28,6 @@ left = (yy <= 0.75/0.5 * dim[1]/dim[2] * xx)
right = np.fliplr(left)
mag_shape[0, ...] = np.logical_and(np.logical_and(left, right), bottom)
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi, theta, magnitude))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_random_pixels.py b/scripts/magdata/magcreator/create_random_pixels.py
index ce81436b8a85d2d681e7a8862bc24b7c6e607ba9..7173694708b94dd49cf627be34a012f05a376653 100644
--- a/scripts/magdata/magcreator/create_random_pixels.py
+++ b/scripts/magdata/magcreator/create_random_pixels.py
@@ -28,11 +28,11 @@ left = (yy <= 0.75/0.5 * dim[1]/dim[2] * xx)
right = np.fliplr(left)
mag_shape[0, ...] = np.logical_and(np.logical_and(left, right), bottom)
-# Create and save MagData object:
-mag_data = py.MagData(a, np.zeros((3,)+dim))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, np.zeros((3,) + dim))
for i in range(count):
pixel = (rnd.randrange(dim[0]), rnd.randrange(dim[1]), rnd.randrange(dim[2]))
mag_shape = py.magcreator.Shapes.pixel(dim, pixel)
phi = 2 * np.pi * rnd.random()
- mag_data += py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi))
+ mag_data += py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_random_slabs.py b/scripts/magdata/magcreator/create_random_slabs.py
index 3bc7a918f9cfd4efda2dfb7a0db64063ebe40173..b68e37477c3105d202947ba1622af99a41db6743 100644
--- a/scripts/magdata/magcreator/create_random_slabs.py
+++ b/scripts/magdata/magcreator/create_random_slabs.py
@@ -29,8 +29,8 @@ left = (yy <= 0.75/0.5 * dim[1]/dim[2] * xx)
right = np.fliplr(left)
mag_shape[0, ...] = np.logical_and(np.logical_and(left, right), bottom)
-# Create and save MagData object:
-mag_data = py.MagData(a, np.zeros((3,)+dim))
+# Create and save VectorData object:
+mag_data = py.VectorData(a, np.zeros((3,) + dim))
for i in range(count):
width = (1, rnd.randint(1, w_max), rnd.randint(1, w_max))
center = (rnd.randrange(int(width[0]/2), dim[0]-int(width[0]/2)),
@@ -38,5 +38,5 @@ for i in range(count):
rnd.randrange(int(width[2]/2), dim[2]-int(width[2]/2)))
mag_shape = py.magcreator.Shapes.slab(dim, center, width)
phi = 2 * np.pi * rnd.random()
- mag_data += py.MagData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi))
+ mag_data += py.VectorData(a, py.magcreator.create_mag_dist_homog(mag_shape, phi))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_singularity.py b/scripts/magdata/magcreator/create_singularity.py
index d050b0e1e0038e0f883c2630c2a09642e955e112..cc69368e33380074e42d95c05199e3d32d6c39d9 100644
--- a/scripts/magdata/magcreator/create_singularity.py
+++ b/scripts/magdata/magcreator/create_singularity.py
@@ -20,7 +20,7 @@ zz, yy, xx = np.indices(dim)
magnitude = np.array((xx-center[2], yy-center[1], zz-center[0]))
magnitude /= np.sqrt((magnitude**2).sum(axis=0))
-# Create and save MagData object:
-mag_data = py.MagData(a, magnitude)
+# Create and save VectorData object:
+mag_data = py.VectorData(a, magnitude)
mag_data.quiver_plot3d(coloring='full angle')
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_vortex_disc.py b/scripts/magdata/magcreator/create_vortex_disc.py
index 4feb7ca0b464ac7daf59752973af6b4072c25aee..72291dcdf4e8533ab2a95e31bf0bba6a4935fc52 100644
--- a/scripts/magdata/magcreator/create_vortex_disc.py
+++ b/scripts/magdata/magcreator/create_vortex_disc.py
@@ -22,6 +22,7 @@ radius = dim[2]//4
height = dim[0]//2
mag_shape = py.magcreator.Shapes.disc(dim, center, radius, height, axis)
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_vortex(mag_shape, center, axis, magnitude))
+# Create and save VectorData object:
+mag_data = py.VectorData(a,
+ py.magcreator.create_mag_dist_vortex(mag_shape, center, axis, magnitude))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magcreator/create_vortex_sphere.py b/scripts/magdata/magcreator/create_vortex_sphere.py
index 0999d30c54b1d216c2caead1e4754b27514e5c7a..2c2ccee577024f43dbb25114527428d5138b8004 100644
--- a/scripts/magdata/magcreator/create_vortex_sphere.py
+++ b/scripts/magdata/magcreator/create_vortex_sphere.py
@@ -21,6 +21,7 @@ center = (dim[0]//2-0.5, dim[1]//2-0.5, dim[2]//2-0.5)
radius = dim[2]//4 # in px
mag_shape = py.magcreator.Shapes.sphere(dim, center, radius)
-# Create and save MagData object:
-mag_data = py.MagData(a, py.magcreator.create_mag_dist_vortex(mag_shape, center, axis, magnitude))
+# Create and save VectorData object:
+mag_data = py.VectorData(a,
+ py.magcreator.create_mag_dist_vortex(mag_shape, center, axis, magnitude))
mag_data.save_to_netcdf4(filename)
diff --git a/scripts/magdata/magdata_from_dat.py b/scripts/magdata/magdata_from_dat.py
index c0fdf10fb30c4546764ef885675e149a9f7dbc30..e698299cfdb1f8359b6b2c8ebb525741505857ae 100644
--- a/scripts/magdata/magdata_from_dat.py
+++ b/scripts/magdata/magdata_from_dat.py
@@ -29,7 +29,7 @@ xmag = xmag.reshape(dim).swapaxes(1, 2)
ymag = ymag.reshape(dim).swapaxes(1, 2)
zmag = zmag.reshape(dim).swapaxes(1, 2)
magnitude = np.array((xmag, ymag, zmag))
-mag_data = py.MagData(a, magnitude)
+mag_data = py.VectorData(a, magnitude)
#mag_data.save_to_netcdf4('magdata_dat_{}'.format(filename.replace('.dat', '.nc')))
mag_data.quiver_plot3d(ar_dens=4, coloring='amplitude')
mag_data.quiver_plot3d(ar_dens=4, coloring='angle')
@@ -57,8 +57,8 @@ py.pm(mag_data).display_combined(interpolation='bilinear')
# xmag = np.reshape(xmag, dim).swapaxes(1, 2)
# ymag = np.reshape(ymag, dim).swapaxes(1, 2)
# zmag = np.reshape(zmag, dim).swapaxes(1, 2)
-# magnitude = np.array((xmag, ymag, zmag))
-# mag_data = py.MagData(a, magnitude)
+# field = np.array((xmag, ymag, zmag))
+# mag_data = py.VectorData(a, field)
# return mag_data
## mag_data.save_to_netcdf4('magdata_dat_{}'.format(filename.replace('.dat', '.nc')))
#
diff --git a/scripts/magdata/magdata_from_txtfortran.py b/scripts/magdata/magdata_from_txtfortran.py
index 912a0f14910602df207a115ec81e7eca5346629b..6a461cdf76a8a440392bd85b2d8714c9496df900 100644
--- a/scripts/magdata/magdata_from_txtfortran.py
+++ b/scripts/magdata/magdata_from_txtfortran.py
@@ -26,6 +26,6 @@ y_mag = np.reshape(data[:, 4], dim, order='F')
z_mag = np.reshape(data[:, 5], dim, order='F')
magnitude = np.array((x_mag, y_mag, z_mag))
-# Create and save MagData object:
-mag_data = py.MagData(a, magnitude)
+# Create and save VectorData object:
+mag_data = py.VectorData(a, magnitude)
mag_data.save_to_netcdf4('magdata_txtfortran_{}'.format(filename.replace('.txt', '.nc')))
diff --git a/scripts/magdata/magdata_from_vtk.py b/scripts/magdata/magdata_from_vtk.py
index 76b3dbae3f4dd780b7d9a34d45355d3fad5949e8..d377aa6917219a14e336101accc3ab69ec1ab858 100644
--- a/scripts/magdata/magdata_from_vtk.py
+++ b/scripts/magdata/magdata_from_vtk.py
@@ -113,13 +113,13 @@ def excluding_mesh(x, y, nx=30, ny=30):
#plt.show()
-# Create empty magnitude:
+# Create empty field:
magnitude = np.zeros((3, len(z), len(y), len(x)), dtype=py.fft.FLOAT)
print 'Mag Dimensions:', magnitude.shape[1:]
#import pdb; pdb.set_trace()
-# Fill magnitude slice per slice:
+# Fill field slice per slice:
for i, zi in tqdm(enumerate(z), total=len(z)):
# Take all points that lie in one z-voxel of the new regular grid into account (use weights!):
z_slice = data[np.abs(data[:, 2]-zi) <= a/2., :]
@@ -150,7 +150,7 @@ for i, zi in tqdm(enumerate(z), total=len(z)):
a *= 10
print 'CREATE AND SAVE MAGDATA OBJECT!'
-mag_data = py.MagData(a, magnitude)
+mag_data = py.VectorData(a, magnitude)
mag_data.save_to_netcdf4('magdata_vtk_{}'.format(filename.replace('.vtk', '.nc')))
-py.pm(mag_data).display_combined()
\ No newline at end of file
+py.pm(mag_data).display_combined()
diff --git a/scripts/phasemap/phasemap_projection_arbitrary.py b/scripts/phasemap/phasemap_projection_arbitrary.py
index e0f7b7b589ee306531dd86d37b304faef51b33bf..baa3fbd81a51a66e60e676cdc3c4f933a2bbbdb1 100644
--- a/scripts/phasemap/phasemap_projection_arbitrary.py
+++ b/scripts/phasemap/phasemap_projection_arbitrary.py
@@ -17,7 +17,7 @@ rotation = np.pi/4.
tilt = 0.
###################################################################################################
-mag_data = py.MagData.load_from_netcdf4(filename)
+mag_data = py.VectorData.load_from_netcdf4(filename)
projector = py.RotTiltProjector(mag_data.dim, rotation, tilt, dim_uv)
mag_proj = projector(mag_data)
phasemapper = py.PhaseMapperRDFC(py.Kernel(mag_data.a, projector.dim_uv, b_0))
diff --git a/scripts/phasemap/phasemap_projection_simple.py b/scripts/phasemap/phasemap_projection_simple.py
index 02c8ee2b49425a66471ea5aedc33de63608bf0f5..1141d660ccb00e6cd291041b7497951172ed4287 100644
--- a/scripts/phasemap/phasemap_projection_simple.py
+++ b/scripts/phasemap/phasemap_projection_simple.py
@@ -14,7 +14,7 @@ b_0 = 1.
dim_uv = None
###################################################################################################
-mag_data = py.MagData.load_from_netcdf4(filename)
+mag_data = py.VectorData.load_from_netcdf4(filename)
phase_map = py.pm(mag_data, dim_uv=dim_uv, b_0=b_0)
phase_map.save_to_netcdf4('phasemap_{}'.format(filename.replace('magdata_', '')))
phase_map.display_combined()
diff --git a/scripts/phasemap/phasemap_tilt_series.py b/scripts/phasemap/phasemap_tilt_series.py
index 06c0d64128588788b0bc706018fbee11c1b305a8..992bcef7352183673387c1bbff932cb5de04576d 100644
--- a/scripts/phasemap/phasemap_tilt_series.py
+++ b/scripts/phasemap/phasemap_tilt_series.py
@@ -18,7 +18,7 @@ dim_uv = None
angles = np.linspace()
###################################################################################################
-mag_data = py.MagData.load_from_netcdf4(filename)
+mag_data = py.VectorData.load_from_netcdf4(filename)
phase_map = py.pm(mag_data, mode=axis, dim_uv=dim_uv, b_0=b_0)
phase_map.save_to_netcdf4('phasemap_{}_axis={}'.format(filename.replace('magdata_', ''), axis))
phase_map.display_combined()
@@ -29,11 +29,11 @@ dim_uv = (500, 200)
angles = np.arange(-60, 61, 5)#[0, 20, 40, 60]
#mag_data_xy = mag_data.copy()
-#mag_data_xy.magnitude[2] = 0
+# mag_data_xy.field[2] = 0
#
#mag_data_z = mag_data.copy()
-#mag_data_z.magnitude[0] = 0
-#mag_data_z.magnitude[1] = 0
+# mag_data_z.field[0] = 0
+# mag_data_z.field[1] = 0
# Iterate over all angles:
for angle in angles:
diff --git a/scripts/reconstruction/reconstruction_3d_from_magdata.py b/scripts/reconstruction/reconstruction_3d_from_magdata.py
index 3d0cb3bc831472f9d07bf279b297ac2ae1230b31..25981c68572a45ef15e2e90f09cb24a356c6690b 100644
--- a/scripts/reconstruction/reconstruction_3d_from_magdata.py
+++ b/scripts/reconstruction/reconstruction_3d_from_magdata.py
@@ -34,7 +34,7 @@ if __name__ == '__main__':
mp.freeze_support()
# Load magnetization distribution:
- mag_data = pr.MagData.load_from_hdf5(mag_name + '.hdf5')
+ mag_data = pr.VectorData.load_from_hdf5(mag_name + '.hdf5')
dim = mag_data.dim
# Construct data set and regularisator: