From 51b39c56825610174ad930f041b2a46863aef203 Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Fri, 22 Apr 2016 00:18:23 +0200
Subject: [PATCH] Updated to work with Python 3! GUIs now import .ui-files
directly.
---
.hgignore | 1 +
.idea/.name | 1 -
.idea/Pyramid.iml | 22 -
.idea/codeStyleSettings.xml | 13 -
.idea/dictionaries/Jan.xml | 3 -
.idea/encodings.xml | 6 -
.idea/inspectionProfiles/Project_Default.xml | 90 -
.../inspectionProfiles/profiles_settings.xml | 7 -
.idea/misc.xml | 14 -
.idea/modules.xml | 12 -
.idea/scopes/__c.xml | 3 -
.idea/scopes/__init__.xml | 3 -
.idea/vcs.xml | 9 -
.idea/workspace.xml | 1500 -----------------
pyramid/__init__.py | 9 +-
pyramid/colormap.py | 4 +-
pyramid/fft.py | 25 +-
pyramid/fielddata.py | 48 +-
pyramid/forwardmodel.py | 4 +-
pyramid/kernel.py | 8 +-
pyramid/magcreator.py | 45 +-
pyramid/phasemap.py | 6 +-
pyramid/phasemapper.py | 7 +-
pyramid/projector.py | 11 +-
pyramid/reconstruction.py | 4 +-
pyramid/regularisator.py | 21 +-
pyramid/tests/test_analytic.py | 13 +-
pyramid/tests/test_dataset.py | 2 -
pyramid/version.py | 6 +-
scripts/gui/mag_slicer.py | 240 +--
scripts/gui/mag_slicer.ui | 457 ++---
scripts/gui/phasemap_creator.py | 205 +--
scripts/gui/phasemap_creator.ui | 403 ++---
scripts/magdata/magdata_from_vtk.py | 7 +-
scripts/phasemap/phasemap_from_dm3.py | 23 +-
scripts/phasemap/phasemap_from_raw.py | 3 +-
.../reconstruction_2d_from_phasemap.py | 11 +-
setup.py | 22 +-
38 files changed, 683 insertions(+), 2585 deletions(-)
delete mode 100644 .idea/.name
delete mode 100644 .idea/Pyramid.iml
delete mode 100644 .idea/codeStyleSettings.xml
delete mode 100644 .idea/dictionaries/Jan.xml
delete mode 100644 .idea/encodings.xml
delete mode 100644 .idea/inspectionProfiles/Project_Default.xml
delete mode 100644 .idea/inspectionProfiles/profiles_settings.xml
delete mode 100644 .idea/misc.xml
delete mode 100644 .idea/modules.xml
delete mode 100644 .idea/scopes/__c.xml
delete mode 100644 .idea/scopes/__init__.xml
delete mode 100644 .idea/vcs.xml
delete mode 100644 .idea/workspace.xml
diff --git a/.hgignore b/.hgignore
index 38bb72d..52b3b62 100644
--- a/.hgignore
+++ b/.hgignore
@@ -13,3 +13,4 @@ files*
build*
Pyramid.egg-info*
logfile.log
+.idea*
diff --git a/.idea/.name b/.idea/.name
deleted file mode 100644
index ad51e80..0000000
--- a/.idea/.name
+++ /dev/null
@@ -1 +0,0 @@
-Pyramid
\ No newline at end of file
diff --git a/.idea/Pyramid.iml b/.idea/Pyramid.iml
deleted file mode 100644
index 5eca370..0000000
--- a/.idea/Pyramid.iml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
- <component name="NewModuleRootManager">
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/pyramid" isTestSource="false" />
- </content>
- <orderEntry type="jdk" jdkName="Python 2.7.11 (C:\Anaconda2\python.exe)" jdkType="Python SDK" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="HyperSpy" />
- <orderEntry type="module" module-name="Jutil" />
- <orderEntry type="module" module-name="Publications" />
- <orderEntry type="module" module-name="Script-Vault" />
- </component>
- <component name="ReSTService">
- <option name="workdir" value="$MODULE_DIR$" />
- <option name="DOC_DIR" value="$MODULE_DIR$" />
- </component>
- <component name="TestRunnerService">
- <option name="projectConfiguration" value="Nosetests" />
- <option name="PROJECT_TEST_RUNNER" value="Nosetests" />
- </component>
-</module>
\ No newline at end of file
diff --git a/.idea/codeStyleSettings.xml b/.idea/codeStyleSettings.xml
deleted file mode 100644
index 7fb8ed0..0000000
--- a/.idea/codeStyleSettings.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="ProjectCodeStyleSettingsManager">
- <option name="PER_PROJECT_SETTINGS">
- <value>
- <XML>
- <option name="XML_LEGACY_SETTINGS_IMPORTED" value="true" />
- </XML>
- </value>
- </option>
- <option name="PREFERRED_PROJECT_CODE_STYLE" value="Default (1)" />
- </component>
-</project>
\ No newline at end of file
diff --git a/.idea/dictionaries/Jan.xml b/.idea/dictionaries/Jan.xml
deleted file mode 100644
index 9a9d8f9..0000000
--- a/.idea/dictionaries/Jan.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<component name="ProjectDictionaryState">
- <dictionary name="Jan" />
-</component>
\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
deleted file mode 100644
index 97626ba..0000000
--- a/.idea/encodings.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="Encoding">
- <file url="PROJECT" charset="UTF-8" />
- </component>
-</project>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
deleted file mode 100644
index 94c0305..0000000
--- a/.idea/inspectionProfiles/Project_Default.xml
+++ /dev/null
@@ -1,90 +0,0 @@
-<component name="InspectionProjectProfileManager">
- <profile version="1.0">
- <option name="myName" value="Project Default" />
- <inspection_tool class="LongLine" enabled="true" level="WARNING" enabled_by_default="true">
- <scope name="*.c" level="WARNING" enabled="false" />
- </inspection_tool>
- <inspection_tool class="PyArgumentListInspection" enabled="true" level="WARNING" enabled_by_default="true">
- <scope name="gui" level="WARNING" enabled="false" />
- </inspection_tool>
- <inspection_tool class="PyAttributeOutsideInitInspection" enabled="false" level="WEAK WARNING" enabled_by_default="false" />
- <inspection_tool class="PyBroadExceptionInspection" enabled="false" level="WEAK WARNING" enabled_by_default="false" />
- <inspection_tool class="PyCallByClassInspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
- <scope name="gui" level="WEAK WARNING" enabled="false" />
- </inspection_tool>
- <inspection_tool class="PyClassicStyleClassInspection" enabled="true" level="WARNING" enabled_by_default="true">
- <scope name="gui" level="WARNING" enabled="false" />
- </inspection_tool>
- <inspection_tool class="PyCompatibilityInspection" enabled="true" level="WARNING" enabled_by_default="true">
- <option name="ourVersions">
- <value>
- <list size="1">
- <item index="0" class="java.lang.String" itemvalue="3.5" />
- </list>
- </value>
- </option>
- </inspection_tool>
- <inspection_tool class="PyMandatoryEncodingInspection" enabled="true" level="WARNING" enabled_by_default="true" />
- <inspection_tool class="PyMissingOrEmptyDocstringInspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
- <scope name="gui" level="WEAK WARNING" enabled="false" />
- </inspection_tool>
- <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
- <scope name="gui" level="WARNING" enabled="false">
- <option name="ignoredPackages">
- <value>
- <list size="0" />
- </value>
- </option>
- </scope>
- <scope name="scripts" level="WARNING" enabled="true">
- <option name="ignoredPackages">
- <value>
- <list size="2">
- <item index="0" class="java.lang.String" itemvalue="pylab" />
- <item index="1" class="java.lang.String" itemvalue="tqdm" />
- </list>
- </value>
- </option>
- </scope>
- <option name="ignoredPackages">
- <value>
- <list size="1">
- <item index="0" class="java.lang.String" itemvalue="hyperspy" />
- </list>
- </value>
- </option>
- </inspection_tool>
- <inspection_tool class="PyPep8Inspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
- <scope name="__init__" level="WEAK WARNING" enabled="true">
- <option name="ignoredErrors">
- <list>
- <option value="E402" />
- </list>
- </option>
- </scope>
- <option name="ignoredErrors">
- <list>
- <option value="W503" />
- </list>
- </option>
- </inspection_tool>
- <inspection_tool class="PyPep8NamingInspection" enabled="false" level="WEAK WARNING" enabled_by_default="false" />
- <inspection_tool class="PyShadowingNamesInspection" enabled="false" level="WEAK WARNING" enabled_by_default="false" />
- <inspection_tool class="PyTypeCheckerInspection" enabled="false" level="WARNING" enabled_by_default="false" />
- <inspection_tool class="PyUnresolvedReferencesInspection" enabled="true" level="WARNING" enabled_by_default="true">
- <scope name="__init__" level="WARNING" enabled="false" />
- <option name="ignoredIdentifiers">
- <list>
- <option value="multiprocessing" />
- <option value="hyperspy.api" />
- </list>
- </option>
- </inspection_tool>
- <inspection_tool class="SpellCheckingInspection" enabled="false" level="TYPO" enabled_by_default="false">
- <option name="processCode" value="true" />
- <option name="processLiterals" value="true" />
- <option name="processComments" value="true" />
- </inspection_tool>
- <inspection_tool class="TodoComment" enabled="false" level="INFO" enabled_by_default="false" />
- </profile>
-</component>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
deleted file mode 100644
index 6933c1e..0000000
--- a/.idea/inspectionProfiles/profiles_settings.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<component name="InspectionProjectProfileManager">
- <settings>
- <option name="PROJECT_PROFILE" value="Project Default" />
- <option name="USE_PROJECT_PROFILE" value="true" />
- <version value="1.0" />
- </settings>
-</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index 2cc28d3..0000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="ProjectLevelVcsManager" settingsEditedManually="false">
- <OptionsSetting value="true" id="Add" />
- <OptionsSetting value="true" id="Remove" />
- <OptionsSetting value="true" id="Checkout" />
- <OptionsSetting value="true" id="Update" />
- <OptionsSetting value="true" id="Status" />
- <OptionsSetting value="true" id="Edit" />
- <ConfirmationsSetting value="0" id="Add" />
- <ConfirmationsSetting value="0" id="Remove" />
- </component>
- <component name="ProjectRootManager" version="2" project-jdk-name="Python 2.7.11 (C:\Anaconda2\python.exe)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index 77d9492..0000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="ProjectModuleManager">
- <modules>
- <module fileurl="file://$PROJECT_DIR$/../HyperSpy/.idea/HyperSpy.iml" filepath="$PROJECT_DIR$/../HyperSpy/.idea/HyperSpy.iml" />
- <module fileurl="file://$PROJECT_DIR$/../Jutil/.idea/Jutil.iml" filepath="$PROJECT_DIR$/../Jutil/.idea/Jutil.iml" />
- <module fileurl="file://$PROJECT_DIR$/../Publications/.idea/Publications.iml" filepath="$PROJECT_DIR$/../Publications/.idea/Publications.iml" />
- <module fileurl="file://$PROJECT_DIR$/.idea/Pyramid.iml" filepath="$PROJECT_DIR$/.idea/Pyramid.iml" />
- <module fileurl="file://$PROJECT_DIR$/../Script-Vault/.idea/Script-Vault.iml" filepath="$PROJECT_DIR$/../Script-Vault/.idea/Script-Vault.iml" />
- </modules>
- </component>
-</project>
\ No newline at end of file
diff --git a/.idea/scopes/__c.xml b/.idea/scopes/__c.xml
deleted file mode 100644
index 29b9103..0000000
--- a/.idea/scopes/__c.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<component name="DependencyValidationManager">
- <scope name="*.c" pattern="file[Pyramid]:pyramid/numcore/*.c" />
-</component>
\ No newline at end of file
diff --git a/.idea/scopes/__init__.xml b/.idea/scopes/__init__.xml
deleted file mode 100644
index 067b2ec..0000000
--- a/.idea/scopes/__init__.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<component name="DependencyValidationManager">
- <scope name="__init__" pattern="file[Pyramid]:pyramid/__init__.py" />
-</component>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
deleted file mode 100644
index 206c387..0000000
--- a/.idea/vcs.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="VcsDirectoryMappings">
- <mapping directory="" vcs="hg4idea" />
- <mapping directory="$PROJECT_DIR$/../Jutil" vcs="hg4idea" />
- <mapping directory="$PROJECT_DIR$/../Publications" vcs="hg4idea" />
- <mapping directory="$PROJECT_DIR$/../Script-Vault" vcs="hg4idea" />
- </component>
-</project>
\ No newline at end of file
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
deleted file mode 100644
index 50f66b1..0000000
--- a/.idea/workspace.xml
+++ /dev/null
@@ -1,1500 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="AnalysisUIOptions">
- <option name="SCOPE_TYPE" value="3" />
- <option name="ANALYSIS_IN_BACKGROUND" value="true" />
- </component>
- <component name="ChangeListManager">
- <list default="true" id="990252ab-aff5-4ac2-a857-b193d2c46b18" name="Default" comment="Updated long overdue scripts to work with new layout and refactoring!">
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/workspace.xml" afterPath="$PROJECT_DIR$/.idea/workspace.xml" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/pyramid/kernel.py" afterPath="$PROJECT_DIR$/pyramid/kernel.py" />
- <change type="MODIFICATION" beforePath="$PROJECT_DIR$/../Script-Vault/scripts - Alt/test methods/compare_pixel_fields.py" afterPath="$PROJECT_DIR$/../Script-Vault/scripts - Alt/test methods/compare_pixel_fields.py" />
- </list>
- <ignored path="Pyramid.iws" />
- <ignored path=".idea/workspace.xml" />
- <option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
- <option name="TRACKING_ENABLED" value="true" />
- <option name="SHOW_DIALOG" value="false" />
- <option name="HIGHLIGHT_CONFLICTS" value="true" />
- <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
- <option name="LAST_RESOLUTION" value="IGNORE" />
- </component>
- <component name="ChangesViewManager" flattened_view="true" show_ignored="false" />
- <component name="CreatePatchCommitExecutor">
- <option name="PATCH_PATH" value="" />
- </component>
- <component name="ErrorTreeViewConfiguration">
- <option name="autoscrollToSource" value="true" />
- <option name="IS_AUTOSCROLL_TO_SOURCE" value="true" />
- </component>
- <component name="ExecutionTargetManager" SELECTED_TARGET="default_target" />
- <component name="FavoritesManager">
- <favorites_list name="Pyramid" />
- </component>
- <component name="FileEditorManager">
- <leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
- <file leaf-file-name="example_joern.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/collaborations/example_joern.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="patrick_nanowire_reconstruction.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/collaborations/patrick_nanowire_reconstruction.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="patrick_nanowire_reconstruction_simulation.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/collaborations/patrick_nanowire_reconstruction_simulation.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="result.pickle" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/collaborations/result.pickle">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="rueffner_file.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/collaborations/rueffner_file.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="vtk_conversion_nanowire_full.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/collaborations/vtk_conversion_nanowire_full.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="reconstruct_random_pixels.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/reconstruction/reconstruct_random_pixels.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="reconstruction_linear_test.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/reconstruction/reconstruction_linear_test.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="reconstruction_linear_test_batch.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/reconstruction/reconstruction_linear_test_batch.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="reconstruction_sparse_cg_singular_values.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/reconstruction/reconstruction_sparse_cg_singular_values.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="compare_kernels.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/test methods/compare_kernels.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="compare_methods.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/test methods/compare_methods.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="compare_pixel_fields.py" pinned="false" current-in-tab="true">
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/test methods/compare_pixel_fields.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.37866354">
- <caret line="79" column="31" selection-start-line="79" selection-start-column="31" selection-end-line="79" selection-end-column="31" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
- <file leaf-file-name="kernel.py" pinned="false" current-in-tab="false">
- <entry file="file://$PROJECT_DIR$/pyramid/kernel.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="112" column="43" selection-start-line="112" selection-start-column="43" selection-end-line="112" selection-end-column="43" />
- <folding />
- </state>
- </provider>
- </entry>
- </file>
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- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/test methods/compare_methods.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- <entry file="file://$APPLICATION_HOME_DIR$/helpers/pydev/pydev_run_in_console.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="28" column="0" selection-start-line="28" selection-start-column="0" selection-end-line="28" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/../HyperSpy/hyperspy/io.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.33294255">
- <caret line="343" column="0" selection-start-line="343" selection-start-column="0" selection-end-line="343" selection-end-column="0" />
- <folding />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/pyramid/phasemap.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="154" column="16" selection-start-line="154" selection-start-column="16" selection-end-line="154" selection-end-column="16" />
- <folding />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/pyramid/kernel.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.0">
- <caret line="112" column="43" selection-start-line="112" selection-start-column="43" selection-end-line="112" selection-end-column="43" />
- <folding />
- </state>
- </provider>
- </entry>
- <entry file="file://$PROJECT_DIR$/../Script-Vault/scripts - Alt/test methods/compare_pixel_fields.py">
- <provider selected="true" editor-type-id="text-editor">
- <state vertical-scroll-proportion="0.37866354">
- <caret line="79" column="31" selection-start-line="79" selection-start-column="31" selection-end-line="79" selection-end-column="31" />
- <folding />
- </state>
- </provider>
- </entry>
- </component>
- <component name="hg4idea.settings">
- <option name="CHECK_INCOMING_OUTGOING" value="true" />
- <option name="RECENT_HG_ROOT_PATH" value="$PROJECT_DIR$/../Script-Vault" />
- <option name="ROOT_SYNC" value="DONT_SYNC" />
- </component>
- <component name="masterDetails">
- <states>
- <state key="ScopeChooserConfigurable.UI">
- <settings>
- <last-edited>gui</last-edited>
- <splitter-proportions>
- <option name="proportions">
- <list>
- <option value="0.2" />
- </list>
- </option>
- </splitter-proportions>
- <order>
- <scope name="__init__" />
- <scope name="*.c" />
- <scope name="scripts" />
- <scope name="gui" />
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- </state>
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-</project>
\ No newline at end of file
diff --git a/pyramid/__init__.py b/pyramid/__init__.py
index d75f904..48789f4 100644
--- a/pyramid/__init__.py
+++ b/pyramid/__init__.py
@@ -48,13 +48,6 @@ numcore
"""
-import logging
-_log = logging.getLogger(__name__)
-try: # Try importing HyperSpy (here because otherwise API Errors might occur):
- import hyperspy.api
-except ImportError:
- _log.error('Could not load hyperspy package!')
-
from . import analytic
from . import magcreator
from . import reconstruction
@@ -92,6 +85,8 @@ from .config import *
from .version import version as __version__
from .version import hg_revision as __hg_revision__
+import logging
+_log = logging.getLogger(__name__)
_log.info("Starting Pyramid V{} HG{}".format(__version__, __hg_revision__))
del logging
diff --git a/pyramid/colormap.py b/pyramid/colormap.py
index 55543fa..73147b7 100644
--- a/pyramid/colormap.py
+++ b/pyramid/colormap.py
@@ -83,7 +83,7 @@ class DirectionalColormap(colors.LinearSegmentedColormap):
def __init__(self, inverted=False):
self._log.debug('Calling __create_directional_colormap')
cdict = self.CDICT_INV if inverted else self.CDICT
- super(DirectionalColormap, self).__init__('directional_colormap', cdict, N=256)
+ super().__init__('directional_colormap', cdict, N=256)
self._log.debug('Created ' + str(self))
@classmethod
@@ -250,5 +250,5 @@ class TransparentColormap(colors.LinearSegmentedColormap):
blue = [(0., 0., b), (1., b, 1.)]
alpha = [(0., 0., alpha_range[0]), (1., alpha_range[1], 1.)]
cdict = {'red': red, 'green': green, 'blue': blue, 'alpha': alpha}
- super(TransparentColormap, self).__init__('transparent_colormap', cdict, N=256)
+ super().__init__('transparent_colormap', cdict, N=256)
self._log.debug('Created ' + str(self))
diff --git a/pyramid/fft.py b/pyramid/fft.py
index f81d867..7ca01fc 100644
--- a/pyramid/fft.py
+++ b/pyramid/fft.py
@@ -11,10 +11,8 @@ FFT operations.
"""
-try:
- import cPickle as pickle
-except ImportError:
- import pickle
+
+import pickle
import logging
import os
@@ -22,28 +20,19 @@ import numpy as np
from pyramid.config import NTHREADS
-# pyFFTW depends on this
-# try:
-# from collections import Counter
-# except ImportError:
-# from collections_python27 import Counter
-# import collections
-#
-# collections.Counter = Counter
+_log = logging.getLogger(__name__)
try:
import pyfftw
-
BACKEND = 'fftw'
except ImportError:
pyfftw = None
BACKEND = 'numpy'
- print("pyFFTW module not found. Using numpy implementation.")
+ _log.info('pyFFTW module not found. Using numpy implementation.')
__all__ = ['PLANS', 'FLOAT', 'COMPLEX', 'dump_wisdom', 'load_wisdom', # analysis:ignore
'zeros', 'empty', 'configure_backend',
'fftn', 'ifftn', 'rfftn', 'irfftn', 'rfftn_adj', 'irfftn_adj']
-_log = logging.getLogger(__name__)
class FFTWCache(object):
@@ -384,6 +373,12 @@ def configure_backend(backend):
# On import:
+ifftn = None
+fftn = None
+rfftn = None
+irfftn = None
+rfftn_adj = None
+irfftn_adj = None
if pyfftw is not None:
configure_backend('fftw')
else:
diff --git a/pyramid/fielddata.py b/pyramid/fielddata.py
index af6881e..e08aa9f 100644
--- a/pyramid/fielddata.py
+++ b/pyramid/fielddata.py
@@ -6,19 +6,18 @@
from __future__ import division
-from scipy.ndimage.interpolation import zoom
-
-from pyramid import fft
-from pyramid.colormap import DirectionalColormap
-
+import abc
import logging
import os
-from abc import ABCMeta, abstractmethod
from numbers import Number
import numpy as np
from matplotlib import pyplot as plt
from matplotlib.ticker import MaxNLocator
+from scipy.ndimage.interpolation import zoom
+
+from pyramid import fft
+from pyramid.colormap import DirectionalColormap
_log = logging.getLogger(__name__)
try: # Try importing HyperSpy:
@@ -30,7 +29,7 @@ except ImportError:
__all__ = ['VectorData', 'ScalarData']
-class FieldData(object):
+class FieldData(object, metaclass=abc.ABCMeta):
"""Class for storing field data.
Abstract base class for the representatio of magnetic or electric fields (see subclasses).
@@ -50,7 +49,6 @@ class FieldData(object):
"""
- __metaclass__ = ABCMeta
_log = logging.getLogger(__name__ + '.FieldData')
@property
@@ -231,7 +229,7 @@ class FieldData(object):
mlab.orientation_axes()
return plot
- @abstractmethod
+ @abc.abstractmethod
def scale_down(self, n):
"""Scale down the field distribution by averaging over two pixels along each axis.
@@ -252,7 +250,7 @@ class FieldData(object):
"""
pass
- @abstractmethod
+ @abc.abstractmethod
def scale_up(self, n, order):
"""Scale up the field distribution using spline interpolation of the requested order.
@@ -275,7 +273,7 @@ class FieldData(object):
"""
pass
- @abstractmethod
+ @abc.abstractmethod
def get_vector(self, mask):
"""Returns the field as a vector, specified by a mask.
@@ -292,7 +290,7 @@ class FieldData(object):
"""
pass
- @abstractmethod
+ @abc.abstractmethod
def set_vector(self, vector, mask):
"""Set the field of the masked pixels to the values specified by `vector`.
@@ -310,7 +308,7 @@ class FieldData(object):
"""
pass
- @abstractmethod
+ @abc.abstractmethod
def to_signal(self):
"""Convert :class:`~.FieldData` data into a HyperSpy signal.
@@ -326,7 +324,7 @@ class FieldData(object):
"""
pass
- @abstractmethod
+ @abc.abstractmethod
def save_to_hdf5(self, filename, *args, **kwargs):
"""Save field data in a file with HyperSpys HDF5-format.
@@ -365,11 +363,6 @@ class VectorData(FieldData):
"""
_log = logging.getLogger(__name__ + '.VectorData')
- def __init__(self, a, field):
- self._log.debug('Calling __init__')
- super(VectorData, self).__init__(a, field)
- self._log.debug('Created ' + str(self))
-
def scale_down(self, n=1):
"""Scale down the field distribution by averaging over two pixels along each axis.
@@ -389,7 +382,7 @@ class VectorData(FieldData):
"""
self._log.debug('Calling scale_down')
- assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
+ assert n > 0 and isinstance(n, int), 'n must be a positive integer!'
self.a *= 2 ** n
for t in range(n):
# Pad if necessary:
@@ -422,8 +415,8 @@ class VectorData(FieldData):
Acts in place and changes dimensions and grid spacing accordingly.
"""
self._log.debug('Calling scale_up')
- assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
- assert 5 > order >= 0 and isinstance(order, (int, long)), \
+ assert n > 0 and isinstance(n, int), 'n must be a positive integer!'
+ assert 5 > order >= 0 and isinstance(order, int), \
'order must be a positive integer between 0 and 5!'
self.a /= 2 ** n
self.field = np.array((zoom(self.field[0], zoom=2 ** n, order=order),
@@ -1056,11 +1049,6 @@ class ScalarData(FieldData):
"""
_log = logging.getLogger(__name__ + '.ScalarData')
- def __init__(self, a, field):
- self._log.debug('Calling __init__')
- super(ScalarData, self).__init__(a, field)
- self._log.debug('Created ' + str(self))
-
def scale_down(self, n=1):
"""Scale down the field distribution by averaging over two pixels along each axis.
@@ -1080,7 +1068,7 @@ class ScalarData(FieldData):
"""
self._log.debug('Calling scale_down')
- assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
+ assert n > 0 and isinstance(n, int), 'n must be a positive integer!'
self.a *= 2 ** n
for t in range(n):
# Pad if necessary:
@@ -1112,8 +1100,8 @@ class ScalarData(FieldData):
Acts in place and changes dimensions and grid spacing accordingly.
"""
self._log.debug('Calling scale_up')
- assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
- assert 5 > order >= 0 and isinstance(order, (int, long)), \
+ assert n > 0 and isinstance(n, int), 'n must be a positive integer!'
+ assert 5 > order >= 0 and isinstance(order, int), \
'order must be a positive integer between 0 and 5!'
self.a /= 2 ** n
self.field = zoom(self.field, zoom=2 ** n, order=order)
diff --git a/pyramid/forwardmodel.py b/pyramid/forwardmodel.py
index eca8aca..e09d39a 100644
--- a/pyramid/forwardmodel.py
+++ b/pyramid/forwardmodel.py
@@ -5,7 +5,7 @@
"""This module provides the :class:`~.ForwardModel` class which represents a strategy to map a
threedimensional magnetization distribution onto a two-dimensional phase map."""
-from __future__ import division, print_function
+from __future__ import division
import logging
import multiprocessing as mp
@@ -188,7 +188,7 @@ class DistributedForwardModel(ForwardModel):
def __init__(self, data_set, ramp_order=None, nprocs=1):
# Evoke super constructor to set up the normal ForwardModel:
- super(DistributedForwardModel, self).__init__(data_set, ramp_order)
+ super().__init__(data_set, ramp_order)
# Initialize multirocessing specific stuff:
self.nprocs = nprocs
img_per_proc = np.ceil(self.data_set.count / self.nprocs).astype(np.int)
diff --git a/pyramid/kernel.py b/pyramid/kernel.py
index 1d5a17f..6ff2ac2 100644
--- a/pyramid/kernel.py
+++ b/pyramid/kernel.py
@@ -5,8 +5,6 @@
"""This module provides the :class:`~.Kernel` class, representing the phase contribution of one
single magnetized pixel."""
-from __future__ import print_function
-
import logging
import numpy as np
@@ -89,6 +87,10 @@ class Kernel(object):
self.slice_mag = (slice(0, dim_uv[0]), # Magnetization is padded on the far end!
slice(0, dim_uv[1])) # (Phase cutout is shifted as listed above)
# Calculate kernel (single pixel phase):
+ # [M_0] = [PHI_0 / µ_0] = Tm² / N/A² = N/Am * A²/N = A/m
+ # --> This is the magnetization, not the magnetic moment (A/m * m³ = Am²)!
+ # [b_0] = [µ_0] * [M_0] = A/m * N/A² = N/Am = T
+ # [coeff] = [b_0 * a² / (2*PHI_0)] = T * m² / Tm² = 1 --> without unit (phase)!
coeff = b_0 * a ** 2 / (2 * PHI_0) # Minus is gone because of negative z-direction
v_dim, u_dim = dim_uv
u = np.linspace(-(u_dim - 1), u_dim - 1, num=2 * u_dim - 1)
@@ -141,7 +143,7 @@ class Kernel(object):
None
"""
- self._log.debug('Calling print_info')
+ self._log.debug('Calling log_info')
print('Shape of the FOV :', self.dim_uv)
print('Shape of the Kernel:', self.dim_kern)
print('Zero-padded shape :', self.dim_pad)
diff --git a/pyramid/magcreator.py b/pyramid/magcreator.py
index 20d31d4..e31b44e 100644
--- a/pyramid/magcreator.py
+++ b/pyramid/magcreator.py
@@ -28,7 +28,7 @@ __all__ = ['Shapes', 'create_mag_dist_homog', 'create_mag_dist_vortex']
_log = logging.getLogger(__name__)
-class Shapes(object):
+class Shapes(object, metaclass=abc.ABCMeta):
"""Abstract class containing functions for generating magnetic shapes.
The :class:`~.Shapes` class is a collection of some methods that return a 3-dimensional
@@ -38,11 +38,10 @@ class Shapes(object):
"""
- __metaclass__ = abc.ABCMeta
_log = logging.getLogger(__name__ + '.Shapes')
- @classmethod
- def slab(cls, dim, center, width):
+ @staticmethod
+ def slab(dim, center, width):
"""Create the shape of a slab.
Parameters
@@ -60,7 +59,7 @@ class Shapes(object):
The magnetic shape as a 3D-array with values between 1 and 0.
"""
- cls._log.debug('Calling slab')
+ _log.debug('Calling slab')
assert np.shape(dim) == (3,), 'Parameter dim has to be a tuple of length 3!'
assert np.shape(center) == (3,), 'Parameter center has to be a tuple of length 3!'
assert np.shape(width) == (3,), 'Parameter width has to be a tuple of length 3!'
@@ -70,8 +69,8 @@ class Shapes(object):
zz_shape = np.where(abs(zz - center[0]) <= width[0] / 2, True, False)
return np.logical_and(np.logical_and(xx_shape, yy_shape), zz_shape)
- @classmethod
- def disc(cls, dim, center, radius, height, axis='z'):
+ @staticmethod
+ def disc(dim, center, radius, height, axis='z'):
"""Create the shape of a cylindrical disc in x-, y-, or z-direction.
Parameters
@@ -93,7 +92,7 @@ class Shapes(object):
The magnetic shape as a 3D-array with values between 1 and 0.
"""
- cls._log.debug('Calling disc')
+ _log.debug('Calling disc')
assert np.shape(dim) == (3,), 'Parameter dim has to be a a tuple of length 3!'
assert np.shape(center) == (3,), 'Parameter center has to be a a tuple of length 3!'
assert radius > 0 and np.shape(radius) == (), 'Radius has to be a positive scalar value!'
@@ -114,8 +113,8 @@ class Shapes(object):
return np.logical_and(np.where(np.hypot(uu, vv) <= radius, True, False),
np.where(abs(ww) <= height / 2, True, False))
- @classmethod
- def ellipse(cls, dim, center, width, height, axis='z'):
+ @staticmethod
+ def ellipse(dim, center, width, height, axis='z'):
"""Create the shape of an elliptical cylinder in x-, y-, or z-direction.
Parameters
@@ -137,7 +136,7 @@ class Shapes(object):
The magnetic shape as a 3D-array with values between 1 and 0.
"""
- cls._log.debug('Calling ellipse')
+ _log.debug('Calling ellipse')
assert np.shape(dim) == (3,), 'Parameter dim has to be a a tuple of length 3!'
assert np.shape(center) == (3,), 'Parameter center has to be a a tuple of length 3!'
assert np.shape(width) == (2,), 'Parameter width has to be a a tuple of length 2!'
@@ -159,8 +158,8 @@ class Shapes(object):
return np.logical_and(np.where(distance <= 1, True, False),
np.where(abs(ww) <= height / 2, True, False))
- @classmethod
- def sphere(cls, dim, center, radius):
+ @staticmethod
+ def sphere(dim, center, radius):
"""Create the shape of a sphere.
Parameters
@@ -178,7 +177,7 @@ class Shapes(object):
The magnetic shape as a 3D-array with values between 1 and 0.
"""
- cls._log.debug('Calling sphere')
+ _log.debug('Calling sphere')
assert np.shape(dim) == (3,), 'Parameter dim has to be a a tuple of length 3!'
assert np.shape(center) == (3,), 'Parameter center has to be a a tuple of length 3!'
assert radius > 0 and np.shape(radius) == (), 'Radius has to be a positive scalar value!'
@@ -186,8 +185,8 @@ class Shapes(object):
distance = np.sqrt((xx - center[2]) ** 2 + (yy - center[1]) ** 2 + (zz - center[0]) ** 2)
return np.where(distance <= radius, True, False)
- @classmethod
- def ellipsoid(cls, dim, center, width):
+ @staticmethod
+ def ellipsoid(dim, center, width):
"""Create the shape of an ellipsoid.
Parameters
@@ -205,7 +204,7 @@ class Shapes(object):
The magnetic shape as a 3D-array with values between 1 and 0.
"""
- cls._log.debug('Calling ellipsoid')
+ _log.debug('Calling ellipsoid')
assert np.shape(dim) == (3,), 'Parameter dim has to be a a tuple of length 3!'
assert np.shape(center) == (3,), 'Parameter center has to be a a tuple of length 3!'
assert np.shape(width) == (3,), 'Parameter width has to be a a tuple of length 3!'
@@ -215,8 +214,8 @@ class Shapes(object):
+ ((zz - center[0]) / (width[0] / 2)) ** 2)
return np.where(distance <= 1, True, False)
- @classmethod
- def filament(cls, dim, pos, axis='y'):
+ @staticmethod
+ def filament(dim, pos, axis='y'):
"""Create the shape of a filament.
Parameters
@@ -236,7 +235,7 @@ class Shapes(object):
The magnetic shape as a 3D-array with values between 1 and 0.
"""
- cls._log.debug('Calling filament')
+ _log.debug('Calling filament')
assert np.shape(dim) == (3,), 'Parameter dim has to be a tuple of length 3!'
assert np.shape(pos) == (2,), 'Parameter pos has to be a tuple of length 2!'
assert axis in {'z', 'y', 'x'}, 'Axis has to be x, y or z (as a string)!'
@@ -249,8 +248,8 @@ class Shapes(object):
mag_shape[pos[0], pos[1], :] = 1
return mag_shape
- @classmethod
- def pixel(cls, dim, pixel):
+ @staticmethod
+ def pixel(dim, pixel):
"""Create the shape of a single pixel.
Parameters
@@ -266,7 +265,7 @@ class Shapes(object):
The magnetic shape as a 3D-array with values between 1 and 0.
"""
- cls._log.debug('Calling pixel')
+ _log.debug('Calling pixel')
assert np.shape(dim) == (3,), 'Parameter dim has to be a tuple of length 3!'
assert np.shape(pixel) == (3,), 'Parameter pixel has to be a tuple of length 3!'
mag_shape = np.zeros(dim)
diff --git a/pyramid/phasemap.py b/pyramid/phasemap.py
index 5cd8759..7ba0d79 100644
--- a/pyramid/phasemap.py
+++ b/pyramid/phasemap.py
@@ -289,7 +289,7 @@ class PhaseMap(object):
"""
self._log.debug('Calling scale_down')
- assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
+ assert n > 0 and isinstance(n, int), 'n must be a positive integer!'
self.a *= 2 ** n
for t in range(n):
# Pad if necessary:
@@ -326,8 +326,8 @@ class PhaseMap(object):
"""
self._log.debug('Calling scale_up')
- assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
- assert 5 > order >= 0 and isinstance(order, (int, long)), \
+ assert n > 0 and isinstance(n, int), 'n must be a positive integer!'
+ assert 5 > order >= 0 and isinstance(order, int), \
'order must be a positive integer between 0 and 5!'
self.a /= 2 ** n
self.phase = zoom(self.phase, zoom=2 ** n, order=order)
diff --git a/pyramid/phasemapper.py b/pyramid/phasemapper.py
index b07345a..a94fb3c 100644
--- a/pyramid/phasemapper.py
+++ b/pyramid/phasemapper.py
@@ -30,7 +30,7 @@ Q_E = 1.602E-19 # electron charge in C
C = 2.998E8 # speed of light in m/s
-class PhaseMapper(object):
+class PhaseMapper(object, metaclass=abc.ABCMeta):
"""Abstract base class for the phase calculation from a 2-dimensional distribution.
The :class:`~.PhaseMapper-` class represents a strategy for the phasemapping of a
@@ -42,7 +42,6 @@ class PhaseMapper(object):
"""
- __metaclass__ = abc.ABCMeta
_log = logging.getLogger(__name__ + '.PhaseMapper')
@abc.abstractmethod
@@ -261,11 +260,11 @@ class PhaseMapperRDRC(PhaseMapper):
for j in range(dim_uv[0]):
for i in range(dim_uv[1]):
v_phase = v_phi[dim_uv[0] - 1 - j:(2 * dim_uv[0] - 1) - j,
- dim_uv[1] - 1 - i:(2 * dim_uv[1] - 1) - i]
+ dim_uv[1] - 1 - i:(2 * dim_uv[1] - 1) - i]
if abs(v_mag[j, i]) > self.threshold:
phase += u_mag[j, i] * v_phase
u_phase = u_phi[dim_uv[0] - 1 - j:(2 * dim_uv[0] - 1) - j,
- dim_uv[1] - 1 - i:(2 * dim_uv[1] - 1) - i]
+ dim_uv[1] - 1 - i:(2 * dim_uv[1] - 1) - i]
if abs(u_mag[j, i]) > self.threshold:
phase -= v_mag[j, i] * u_phase
# Return the phase:
diff --git a/pyramid/projector.py b/pyramid/projector.py
index 986c18f..30e2f5e 100644
--- a/pyramid/projector.py
+++ b/pyramid/projector.py
@@ -22,7 +22,7 @@ from pyramid.quaternion import Quaternion
__all__ = ['RotTiltProjector', 'XTiltProjector', 'YTiltProjector', 'SimpleProjector']
-class Projector(object):
+class Projector(object, metaclass=abc.ABCMeta):
"""Abstract base class representing a projection function.
The :class:`~.Projector` class represents a projection function for a 3-dimensional
@@ -56,7 +56,6 @@ class Projector(object):
"""
- __metaclass__ = abc.ABCMeta
_log = logging.getLogger(__name__ + '.Projector')
@abc.abstractmethod
@@ -301,7 +300,7 @@ class RotTiltProjector(Projector):
weights = csr_matrix(coo_matrix((data, (rows, columns)), shape=shape))
# Calculate coefficients by rotating unity matrix (unit vectors, (x,y,z)):
coeff = quat.matrix[:2, :].dot(np.eye(3))
- super(RotTiltProjector, self).__init__(dim, dim_uv, weights, coeff)
+ super().__init__(dim, dim_uv, weights, coeff)
self._log.debug('Created ' + str(self))
@staticmethod
@@ -420,7 +419,7 @@ class XTiltProjector(Projector):
self.sparsity = 1. - len(data) / np.prod(shape, dtype=np.float)
weight = csr_matrix(coo_matrix((np.tile(data, dim_rot), (rows, columns)), shape=shape))
coeff = [[1, 0, 0], [0, np.cos(tilt), np.sin(tilt)]]
- super(XTiltProjector, self).__init__(dim, dim_uv, weight, coeff)
+ super().__init__(dim, dim_uv, weight, coeff)
self._log.debug('Created ' + str(self))
@staticmethod
@@ -537,7 +536,7 @@ class YTiltProjector(Projector):
self.sparsity = 1. - len(data) / np.prod(shape, dtype=np.float)
weight = csr_matrix(coo_matrix((np.tile(data, dim_rot), (rows, columns)), shape=shape))
coeff = [[np.cos(tilt), 0, np.sin(tilt)], [0, 1, 0]]
- super(YTiltProjector, self).__init__(dim, dim_uv, weight, coeff)
+ super().__init__(dim, dim_uv, weight, coeff)
self._log.debug('Created ' + str(self))
@staticmethod
@@ -664,7 +663,7 @@ class SimpleProjector(Projector):
shape = (np.prod(dim_uv), np.prod(dim))
self.sparsity = 1. - len(data) / np.prod(shape, dtype=np.float)
weight = csr_matrix((data, indices, indptr), shape=shape)
- super(SimpleProjector, self).__init__(dim, dim_uv, weight, coeff)
+ super().__init__(dim, dim_uv, weight, coeff)
self._log.debug('Created ' + str(self))
def get_info(self, verbose=False):
diff --git a/pyramid/reconstruction.py b/pyramid/reconstruction.py
index 8fe34f1..166242e 100644
--- a/pyramid/reconstruction.py
+++ b/pyramid/reconstruction.py
@@ -43,9 +43,9 @@ def optimize_linear(costfunction, max_iter=None):
"""
import jutil.cg as jcg
_log.debug('Calling optimize_linear')
- _log.info('Cost before optimization: {}'.format(costfunction(np.zeros(costfunction.n))))
+ _log.info('Cost before optimization: {:.3e}'.format(costfunction(np.zeros(costfunction.n))))
x_opt = jcg.conj_grad_minimize(costfunction, max_iter=max_iter).x
- _log.info('Cost after optimization: {}'.format(costfunction(x_opt)))
+ _log.info('Cost after optimization: {:.3e}'.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 VectorData object:
diff --git a/pyramid/regularisator.py b/pyramid/regularisator.py
index 0952cbf..335cd36 100644
--- a/pyramid/regularisator.py
+++ b/pyramid/regularisator.py
@@ -18,7 +18,7 @@ __all__ = ['NoneRegularisator', 'ZeroOrderRegularisator', 'FirstOrderRegularisat
'ComboRegularisator']
-class Regularisator(object):
+class Regularisator(object, metaclass=abc.ABCMeta):
"""Class for providing a regularisation term which implements additional constraints.
Represents a certain constraint for the 3D magnetization distribution whose cost is to minimize
@@ -40,7 +40,6 @@ class Regularisator(object):
"""
- __metaclass__ = abc.ABCMeta
_log = logging.getLogger(__name__ + '.Regularisator')
@abc.abstractmethod
@@ -150,7 +149,7 @@ class ComboRegularisator(Regularisator):
def __init__(self, reg_list):
self._log.debug('Calling __init__')
self.reg_list = reg_list
- super(ComboRegularisator, self).__init__(norm=None, lam=None)
+ super().__init__(norm=None, lam=None)
self._log.debug('Created ' + str(self))
def __call__(self, x):
@@ -246,7 +245,7 @@ class NoneRegularisator(Regularisator):
self.norm = None
self.lam = 0
self.add_params = None
- super(NoneRegularisator, self).__init__(norm=None, lam=None)
+ super().__init__(norm=None, lam=None)
self._log.debug('Created ' + str(self))
def __call__(self, x):
@@ -324,19 +323,22 @@ class ZeroOrderRegularisator(Regularisator):
Regularisation parameter determining the weighting between measurements and regularisation.
p: int, optional
Order of the norm (default: 2, which means a standard L2-norm).
+ add_params : int
+ Number of additional parameters which are not used in the regularisation. Used to cut
+ the input vector into the appropriate size.
"""
_log = logging.getLogger(__name__ + '.ZeroOrderRegularisator')
- def __init__(self, _=None, lam=1E-4, p=2, add_params=None):
+ def __init__(self, _=None, lam=1E-4, p=2, add_params=0):
self._log.debug('Calling __init__')
self.p = p
if p == 2:
norm = jnorm.L2Square()
else:
norm = jnorm.LPPow(p, 1e-12)
- super(ZeroOrderRegularisator, self).__init__(norm, lam, add_params)
+ super().__init__(norm, lam, add_params)
self._log.debug('Created ' + str(self))
@@ -356,10 +358,13 @@ class FirstOrderRegularisator(Regularisator):
Regularisation parameter determining the weighting between measurements and regularisation.
p: int, optional
Order of the norm (default: 2, which means a standard L2-norm).
+ add_params : int
+ Number of additional parameters which are not used in the regularisation. Used to cut
+ the input vector into the appropriate size.
"""
- def __init__(self, mask, lam=1E-4, p=2, add_params=None):
+ def __init__(self, mask, lam=1E-4, p=2, add_params=0):
self.p = p
D0 = jdiff.get_diff_operator(mask, 0, 3)
D1 = jdiff.get_diff_operator(mask, 1, 3)
@@ -369,5 +374,5 @@ class FirstOrderRegularisator(Regularisator):
norm = jnorm.WeightedL2Square(D)
else:
norm = jnorm.WeightedTV(jnorm.LPPow(p, 1e-12), D, [D0.shape[0], D.shape[0]])
- super(FirstOrderRegularisator, self).__init__(norm, lam, add_params)
+ super().__init__(norm, lam, add_params)
self._log.debug('Created ' + str(self))
diff --git a/pyramid/tests/test_analytic.py b/pyramid/tests/test_analytic.py
index 401a4f2..9fd4704 100644
--- a/pyramid/tests/test_analytic.py
+++ b/pyramid/tests/test_analytic.py
@@ -26,7 +26,8 @@ class TestCaseAnalytic(unittest.TestCase):
width = (self.dim[0] / 2, self.dim[1] / 2, self.dim[2] / 2)
phase = an.phase_mag_slab(self.dim, self.a, self.phi, self.center, width).phase
reference = np.load(os.path.join(self.path, 'ref_phase_slab.npy'))
- assert_allclose(phase, reference, err_msg='Unexpected behavior in phase_mag_slab()')
+ assert_allclose(phase, reference, atol=1E-10,
+ err_msg='Unexpected behavior in phase_mag_slab()')
def test_phase_mag_disc(self):
"""Test of the phase_mag_disc method."""
@@ -34,15 +35,16 @@ class TestCaseAnalytic(unittest.TestCase):
height = self.dim[2] / 2
phase = an.phase_mag_disc(self.dim, self.a, self.phi, self.center, radius, height).phase
reference = np.load(os.path.join(self.path, 'ref_phase_disc.npy'))
- assert_allclose(phase, reference, err_msg='Unexpected behavior in phase_mag_disc()')
+ assert_allclose(phase, reference, atol=1E-10,
+ err_msg='Unexpected behavior in phase_mag_disc()')
def test_phase_mag_sphere(self):
"""Test of the phase_mag_sphere method."""
radius = self.dim[2] / 4
phase = an.phase_mag_sphere(self.dim, self.a, self.phi, self.center, radius).phase
reference = np.load(os.path.join(self.path, 'ref_phase_sphere.npy'))
- assert_allclose(phase, reference, err_msg='Unexpected behavior in phase_mag_sphere()',
- atol=1E-10)
+ assert_allclose(phase, reference, atol=1E-10,
+ err_msg='Unexpected behavior in phase_mag_sphere()')
def test_phase_mag_vortex(self):
"""Test of the phase_mag_vortex method."""
@@ -50,7 +52,8 @@ class TestCaseAnalytic(unittest.TestCase):
height = self.dim[2] / 2
phase = an.phase_mag_vortex(self.dim, self.a, self.center, radius, height).phase
reference = np.load(os.path.join(self.path, 'ref_phase_vort.npy'))
- assert_allclose(phase, reference, err_msg='Unexpected behavior in phase_mag_vortex()')
+ assert_allclose(phase, reference, atol=1E-10,
+ err_msg='Unexpected behavior in phase_mag_vortex()')
if __name__ == '__main__':
diff --git a/pyramid/tests/test_dataset.py b/pyramid/tests/test_dataset.py
index 8cb02ab..115eb71 100644
--- a/pyramid/tests/test_dataset.py
+++ b/pyramid/tests/test_dataset.py
@@ -1,8 +1,6 @@
# -*- coding: utf-8 -*-
"""Testcase for the dataset module"""
-from __future__ import print_function
-
import os
import unittest
diff --git a/pyramid/version.py b/pyramid/version.py
index e047f28..2595067 100644
--- a/pyramid/version.py
+++ b/pyramid/version.py
@@ -1,4 +1,4 @@
# -*- coding: utf-8 -*-
-"""This file is generated automatically by the Pyramid `setup.pr`"""
-version = '0.1.0-dev'
-hg_revision = 'a7afcc233730+'
+""""This file is generated automatically by the Pyramid `setup.py`"""
+version = "0.1.0-dev"
+hg_revision = "b'111e1118104a+'"
diff --git a/scripts/gui/mag_slicer.py b/scripts/gui/mag_slicer.py
index e0a46f6..90e3476 100644
--- a/scripts/gui/mag_slicer.py
+++ b/scripts/gui/mag_slicer.py
@@ -10,181 +10,64 @@
import os
import sys
-import pyramid
-from pyramid.fielddata import VectorData
-from pyramid.kernel import Kernel
-from pyramid.phasemapper import PhaseMapperRDFC
-from pyramid.projector import SimpleProjector
+from PyQt4 import QtGui, QtCore
+from PyQt4.uic import loadUiType
-from PyQt4 import QtCore, QtGui
-from matplotlibwidget import MatplotlibWidget
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
-try:
- _fromUtf8 = QtCore.QString.fromUtf8
-except AttributeError:
- def _fromUtf8(s):
- return s
+import pyramid as pr
-try:
- _encoding = QtGui.QApplication.UnicodeUTF8
+UI_MainWindow, QMainWindow = loadUiType('mag_slicer.ui')
- def _translate(context, text, disambig):
- return QtGui.QApplication.translate(context, text, disambig, _encoding)
-except AttributeError:
+class Main(QMainWindow, UI_MainWindow):
- def _translate(context, text, disambig):
- return QtGui.QApplication.translate(context, text, disambig)
-
-
-class UI_MagSlicerMain(QtGui.QWidget):
- def __init__(self, parent=None):
- QtGui.QWidget.__init__(self, parent)
- Form = self
- self.setGeometry(100, 100, 1405, 550)
- self.setWindowTitle('Mag Slicer')
- ###########################################################################################
- self.verticalLayout = QtGui.QVBoxLayout(Form)
- self.verticalLayout.setObjectName(_fromUtf8("verticalLayout"))
- self.horizontalLayout = QtGui.QHBoxLayout()
- self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
- self.pushButtonLoad = QtGui.QPushButton(Form)
- self.pushButtonLoad.setObjectName(_fromUtf8("pushButtonLoad"))
- self.horizontalLayout.addWidget(self.pushButtonLoad)
- self.checkBoxScale = QtGui.QCheckBox(Form)
- self.checkBoxScale.setChecked(True)
- self.checkBoxScale.setTristate(False)
- self.checkBoxScale.setObjectName(_fromUtf8("checkBoxScale"))
- self.horizontalLayout.addWidget(self.checkBoxScale)
- self.checkBoxLog = QtGui.QCheckBox(Form)
- self.checkBoxLog.setObjectName(_fromUtf8("checkBoxLog"))
- self.horizontalLayout.addWidget(self.checkBoxLog)
- self.comboBoxSlice = QtGui.QComboBox(Form)
- self.comboBoxSlice.setObjectName(_fromUtf8("comboBoxSlice"))
- self.comboBoxSlice.addItem(_fromUtf8(""))
- self.comboBoxSlice.addItem(_fromUtf8(""))
- self.comboBoxSlice.addItem(_fromUtf8(""))
- self.horizontalLayout.addWidget(self.comboBoxSlice)
- self.labelSlice = QtGui.QLabel(Form)
- self.labelSlice.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignTrailing |
- QtCore.Qt.AlignVCenter)
- self.labelSlice.setObjectName(_fromUtf8("labelSlice"))
- self.horizontalLayout.addWidget(self.labelSlice)
- self.spinBoxSlice = QtGui.QSpinBox(Form)
- self.spinBoxSlice.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignTrailing |
- QtCore.Qt.AlignVCenter)
- self.spinBoxSlice.setMaximum(0)
- self.spinBoxSlice.setProperty("value", 0)
- self.spinBoxSlice.setObjectName(_fromUtf8("spinBoxSlice"))
- self.horizontalLayout.addWidget(self.spinBoxSlice)
- self.scrollBarSlice = QtGui.QScrollBar(Form)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Fixed)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.scrollBarSlice.sizePolicy().hasHeightForWidth())
- self.scrollBarSlice.setSizePolicy(sizePolicy)
- self.scrollBarSlice.setMinimumSize(QtCore.QSize(400, 0))
- self.scrollBarSlice.setMaximum(0)
- self.scrollBarSlice.setOrientation(QtCore.Qt.Horizontal)
- self.scrollBarSlice.setObjectName(_fromUtf8("scrollBarSlice"))
- self.horizontalLayout.addWidget(self.scrollBarSlice)
- self.checkBoxSmooth = QtGui.QCheckBox(Form)
- self.checkBoxSmooth.setChecked(True)
- self.checkBoxSmooth.setObjectName(_fromUtf8("checkBoxSmooth"))
- self.horizontalLayout.addWidget(self.checkBoxSmooth)
- self.checkBoxAuto = QtGui.QCheckBox(Form)
- self.checkBoxAuto.setChecked(True)
- self.checkBoxAuto.setObjectName(_fromUtf8("checkBoxAuto"))
- self.horizontalLayout.addWidget(self.checkBoxAuto)
- self.labelGain = QtGui.QLabel(Form)
- self.labelGain.setObjectName(_fromUtf8("labelGain"))
- self.horizontalLayout.addWidget(self.labelGain)
- self.spinBoxGain = QtGui.QDoubleSpinBox(Form)
- self.spinBoxGain.setEnabled(False)
- self.spinBoxGain.setMaximum(1000000.0)
- self.spinBoxGain.setSingleStep(0.1)
- self.spinBoxGain.setProperty("value", 1.0)
- self.spinBoxGain.setObjectName(_fromUtf8("spinBoxGain"))
- self.horizontalLayout.addWidget(self.spinBoxGain)
- self.verticalLayout.addLayout(self.horizontalLayout)
- self.horizontalLayoutPlots = QtGui.QHBoxLayout()
- self.horizontalLayoutPlots.setSpacing(0)
- self.horizontalLayoutPlots.setSizeConstraint(QtGui.QLayout.SetNoConstraint)
- self.horizontalLayoutPlots.setObjectName(_fromUtf8("horizontalLayoutPlots"))
- self.mplWidgetMag = MatplotlibWidget(Form)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Ignored, QtGui.QSizePolicy.Expanding)
- sizePolicy.setHorizontalStretch(10)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.mplWidgetMag.sizePolicy().hasHeightForWidth())
- self.mplWidgetMag.setSizePolicy(sizePolicy)
- self.mplWidgetMag.setCursor(QtGui.QCursor(QtCore.Qt.ArrowCursor))
- self.mplWidgetMag.setLayoutDirection(QtCore.Qt.LeftToRight)
- self.mplWidgetMag.setAutoFillBackground(False)
- self.mplWidgetMag.setObjectName(_fromUtf8("mplWidgetMag"))
- self.horizontalLayoutPlots.addWidget(self.mplWidgetMag)
- self.mplWidgetHolo = MatplotlibWidget(Form)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Ignored, QtGui.QSizePolicy.Expanding)
- sizePolicy.setHorizontalStretch(10)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.mplWidgetHolo.sizePolicy().hasHeightForWidth())
- self.mplWidgetHolo.setSizePolicy(sizePolicy)
- self.mplWidgetHolo.setObjectName(_fromUtf8("mplWidgetHolo"))
- self.horizontalLayoutPlots.addWidget(self.mplWidgetHolo)
- self.mplWidgetPhase = MatplotlibWidget(Form)
- self.mplWidgetPhase.setEnabled(True)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Ignored, QtGui.QSizePolicy.Expanding)
- sizePolicy.setHorizontalStretch(10)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.mplWidgetPhase.sizePolicy().hasHeightForWidth())
- self.mplWidgetPhase.setSizePolicy(sizePolicy)
- self.mplWidgetPhase.setObjectName(_fromUtf8("mplWidgetPhase"))
- self.horizontalLayoutPlots.addWidget(self.mplWidgetPhase)
- self.verticalLayout.addLayout(self.horizontalLayoutPlots)
- ###########################################################################################
- self.retranslateUi(Form)
- self.connect(self.spinBoxSlice, QtCore.SIGNAL(_fromUtf8("editingFinished()")),
- self.scrollBarSlice.setValue)
- self.connect(self.scrollBarSlice, QtCore.SIGNAL(_fromUtf8("valueChanged(int)")),
- self.spinBoxSlice.setValue)
- self.connect(self.checkBoxAuto, QtCore.SIGNAL(_fromUtf8("toggled(bool)")),
- self.spinBoxGain.setDisabled)
- self.connect(self.checkBoxLog, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ def __init__(self):
+ super().__init__()
+ self.setupUi(self)
+ self.connect(self.checkBoxLog, QtCore.SIGNAL('clicked()'),
self.update_slice)
- self.connect(self.checkBoxScale, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.connect(self.checkBoxScale, QtCore.SIGNAL('clicked()'),
self.update_slice)
- self.connect(self.spinBoxSlice, QtCore.SIGNAL(_fromUtf8('valueChanged(int)')),
+ self.connect(self.spinBoxSlice, QtCore.SIGNAL('valueChanged(int)'),
self.update_slice)
- self.connect(self.comboBoxSlice, QtCore.SIGNAL(_fromUtf8('currentIndexChanged(int)')),
+ self.connect(self.comboBoxSlice, QtCore.SIGNAL('currentIndexChanged(int)'),
self.update_phase)
- self.connect(self.spinBoxGain, QtCore.SIGNAL(_fromUtf8('editingFinished()')),
+ self.connect(self.spinBoxGain, QtCore.SIGNAL('valueChanged(double)'),
self.update_phase)
- self.connect(self.checkBoxAuto, QtCore.SIGNAL(_fromUtf8('toggled(bool)')),
+ self.connect(self.checkBoxAuto, QtCore.SIGNAL('toggled(bool)'),
self.update_phase)
- self.connect(self.checkBoxSmooth, QtCore.SIGNAL(_fromUtf8('toggled(bool)')),
+ self.connect(self.checkBoxSmooth, QtCore.SIGNAL('toggled(bool)'),
self.update_phase)
- self.connect(self.pushButtonLoad, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.connect(self.pushButtonLoad, QtCore.SIGNAL('clicked()'),
self.load)
- QtCore.QMetaObject.connectSlotsByName(Form)
- self.mplWidgetMag.axes.set_visible(False)
- self.mplWidgetHolo.axes.set_visible(False)
- self.mplWidgetPhase.axes.set_visible(False)
self.mag_data_loaded = False
- def retranslateUi(self, Form):
- ###########################################################################################
- Form.setWindowTitle(_translate("Form", "Mag Slicer", None))
- self.pushButtonLoad.setText(_translate("Form", "Laden", None))
- self.checkBoxScale.setText(_translate("Form", "Scaled", None))
- self.checkBoxLog.setText(_translate("Form", "Log", None))
- self.comboBoxSlice.setItemText(0, _translate("Form", "xy-plane", None))
- self.comboBoxSlice.setItemText(1, _translate("Form", "xz-plane", None))
- self.comboBoxSlice.setItemText(2, _translate("Form", "zy-plane", None))
- self.labelSlice.setText(_translate("Form", "Slice:", None))
- self.checkBoxSmooth.setText(_translate("Form", "Smooth", None))
- self.checkBoxAuto.setText(_translate("Form", "Auto", None))
- self.labelGain.setText(_translate("Form", "Gain:", None))
- ###########################################################################################
+ def addmpl(self):
+ fig = Figure()
+ fig.add_subplot(111, aspect='equal')
+ self.canvasMag = FigureCanvas(fig)
+ self.layoutMag.addWidget(self.canvasMag)
+ self.canvasMag.draw()
+ self.toolbarMag = NavigationToolbar(self.canvasMag, self, coordinates=True)
+ self.layoutMag.addWidget(self.toolbarMag)
+ fig = Figure()
+ fig.add_subplot(111, aspect='equal')
+ self.canvasPhase = FigureCanvas(fig)
+ self.layoutPhase.addWidget(self.canvasPhase)
+ self.canvasPhase.draw()
+ self.toolbarPhase = NavigationToolbar(self.canvasPhase, self, coordinates=True)
+ self.layoutPhase.addWidget(self.toolbarPhase)
+ fig = Figure()
+ fig.add_subplot(111, aspect='equal')
+ self.canvasHolo = FigureCanvas(fig)
+ self.layoutHolo.addWidget(self.canvasHolo)
+ self.canvasHolo.draw()
+ self.toolbarHolo = NavigationToolbar(self.canvasHolo, self, coordinates=True)
+ self.layoutHolo.addWidget(self.toolbarHolo)
def update_phase(self):
if self.mag_data_loaded:
@@ -202,46 +85,51 @@ class UI_MagSlicerMain(QtGui.QWidget):
gain = 'auto'
else:
gain = self.spinBoxGain.value()
- self.projector = SimpleProjector(self.mag_data.dim, axis=self.mode)
+ self.projector = pr.SimpleProjector(self.mag_data.dim, axis=self.mode)
self.spinBoxSlice.setMaximum(length)
self.scrollBarSlice.setMaximum(length)
self.spinBoxSlice.setValue(int(length / 2.))
self.update_slice()
- self.phase_mapper = PhaseMapperRDFC(Kernel(self.mag_data.a, self.projector.dim_uv))
+ kernel = pr.Kernel(self.mag_data.a, self.projector.dim_uv)
+ self.phase_mapper = pr.PhaseMapperRDFC(kernel)
self.phase_map = self.phase_mapper(self.projector(self.mag_data))
- self.phase_map.display_phase(axis=self.mplWidgetPhase.axes, cbar=False)
+ self.canvasPhase.figure.axes[0].clear()
+ self.phase_map.display_phase(axis=self.canvasPhase.figure.axes[0], cbar=False)
if self.checkBoxSmooth.isChecked():
interpolation = 'bilinear'
else:
interpolation = 'none'
- self.phase_map.display_holo(axis=self.mplWidgetHolo.axes, gain=gain,
+ self.canvasHolo.figure.axes[0].clear()
+ self.phase_map.display_holo(axis=self.canvasHolo.figure.axes[0], gain=gain,
interpolation=interpolation)
- self.mplWidgetPhase.draw()
- self.mplWidgetHolo.draw()
+ self.canvasPhase.draw()
+ self.canvasHolo.draw()
def update_slice(self):
if self.mag_data_loaded:
- self.mag_data.quiver_plot(axis=self.mplWidgetMag.axes, proj_axis=self.mode,
+ self.canvasMag.figure.axes[0].clear()
+ self.mag_data.quiver_plot(axis=self.canvasMag.figure.axes[0], proj_axis=self.mode,
ax_slice=self.spinBoxSlice.value(),
log=self.checkBoxLog.isChecked(),
scaled=self.checkBoxScale.isChecked())
- self.mplWidgetMag.draw()
+ self.canvasMag.draw()
def load(self):
- directory = os.path.join(pyramid.DIR_FILES, 'magdata')
- mag_file = QtGui.QFileDialog.getOpenFileName(self, 'Open Data File', directory,
- 'HDF5 files (*.hdf5)')
- self.mag_data = VectorData.load_from_hdf5(mag_file)
+ try:
+ directory = os.path.join(pr.DIR_FILES, 'vecdata')
+ mag_file = QtGui.QFileDialog.getOpenFileName(self, 'Open Data File', directory,
+ 'HDF5 files (*.hdf5)')
+ except ValueError:
+ return # Abort if no conf_path is selected!
+ self.mag_data = pr.VectorData.load_from_hdf5(mag_file)
+ if not self.mag_data_loaded:
+ self.addmpl()
self.mag_data_loaded = True
- self.mplWidgetMag.axes.set_visible(True)
- self.mplWidgetHolo.axes.set_visible(True)
- self.mplWidgetPhase.axes.set_visible(True)
self.comboBoxSlice.setCurrentIndex(0)
self.update_phase()
-
if __name__ == '__main__':
app = QtGui.QApplication(sys.argv)
- widget = UI_MagSlicerMain()
- widget.show()
+ main = Main()
+ main.show()
sys.exit(app.exec_())
diff --git a/scripts/gui/mag_slicer.ui b/scripts/gui/mag_slicer.ui
index 453a95c..bd98387 100644
--- a/scripts/gui/mag_slicer.ui
+++ b/scripts/gui/mag_slicer.ui
@@ -1,224 +1,251 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
- <class>Form</class>
- <widget class="QWidget" name="Form">
+ <class>MainWindow</class>
+ <widget class="QMainWindow" name="MainWindow">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
- <width>993</width>
- <height>351</height>
+ <width>1222</width>
+ <height>480</height>
</rect>
</property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
<property name="windowTitle">
- <string>Mag Slicer</string>
+ <string>MagSlicer</string>
</property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QPushButton" name="pushButtonLoad">
- <property name="text">
- <string>Laden</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxScale">
- <property name="text">
- <string>Scaled</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- <property name="tristate">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxLog">
- <property name="text">
- <string>Log</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBoxSlice">
- <item>
+ <widget class="QWidget" name="centralwidget">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="windowTitle">
+ <string>Mag Slicer</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout">
+ <item>
+ <widget class="QPushButton" name="pushButtonLoad">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
<property name="text">
- <string>xy-plane</string>
+ <string>Laden</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="checkBoxScale">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
</property>
- </item>
- <item>
<property name="text">
- <string>xz-plane</string>
+ <string>Scaled</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ <property name="tristate">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="checkBoxLog">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>Log</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QComboBox" name="comboBoxSlice">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <item>
+ <property name="text">
+ <string>xy-plane</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>xz-plane</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>zy-plane</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="labelSlice">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>Slice:</string>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QSpinBox" name="spinBoxSlice">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
+ </property>
+ <property name="maximum">
+ <number>0</number>
+ </property>
+ <property name="value">
+ <number>0</number>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QScrollBar" name="scrollBarSlice">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>400</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximum">
+ <number>0</number>
+ </property>
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="checkBoxSmooth">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>Smooth</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="checkBoxAuto">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>Auto</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="labelGain">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
</property>
- </item>
- <item>
<property name="text">
- <string>zy-plane</string>
+ <string>Gain:</string>
</property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QDoubleSpinBox" name="spinBoxGain">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="maximum">
+ <double>1000000.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>0.100000000000000</double>
+ </property>
+ <property name="value">
+ <double>1.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <widget class="QWidget" name="layoutPlots" native="true">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Expanding">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <layout class="QHBoxLayout" name="horizontalLayoutPlots">
+ <item>
+ <layout class="QVBoxLayout" name="layoutMag"/>
</item>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="labelSlice">
- <property name="text">
- <string>Slice:</string>
- </property>
- <property name="alignment">
- <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="spinBoxSlice">
- <property name="alignment">
- <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
- </property>
- <property name="maximum">
- <number>0</number>
- </property>
- <property name="value">
- <number>0</number>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QScrollBar" name="scrollBarSlice">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>400</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximum">
- <number>0</number>
- </property>
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxSmooth">
- <property name="text">
- <string>Smooth</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxAuto">
- <property name="text">
- <string>Auto</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="labelGain">
- <property name="text">
- <string>Gain:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinBoxGain">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="maximum">
- <double>1000000.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>1.000000000000000</double>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayoutPlots">
- <property name="spacing">
- <number>0</number>
- </property>
- <property name="sizeConstraint">
- <enum>QLayout::SetNoConstraint</enum>
- </property>
- <item>
- <widget class="MatplotlibWidget" name="mplWidgetMag">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Ignored" vsizetype="Expanding">
- <horstretch>10</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="cursor">
- <cursorShape>ArrowCursor</cursorShape>
- </property>
- <property name="layoutDirection">
- <enum>Qt::LeftToRight</enum>
- </property>
- <property name="autoFillBackground">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="MatplotlibWidget" name="mplWidgetHolo">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Ignored" vsizetype="Expanding">
- <horstretch>10</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="MatplotlibWidget" name="mplWidgetPhase">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Ignored" vsizetype="Expanding">
- <horstretch>10</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
+ <item>
+ <layout class="QVBoxLayout" name="layoutPhase"/>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="layoutHolo"/>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ </layout>
+ </widget>
</widget>
- <customwidgets>
- <customwidget>
- <class>MatplotlibWidget</class>
- <extends>QWidget</extends>
- <header>matplotlibwidget</header>
- </customwidget>
- </customwidgets>
<resources/>
<connections>
<connection>
@@ -228,28 +255,28 @@
<slot>setValue(int)</slot>
<hints>
<hint type="sourcelabel">
- <x>335</x>
- <y>18</y>
+ <x>322</x>
+ <y>19</y>
</hint>
<hint type="destinationlabel">
- <x>380</x>
- <y>17</y>
+ <x>386</x>
+ <y>20</y>
</hint>
</hints>
</connection>
<connection>
<sender>scrollBarSlice</sender>
- <signal>valueChanged(int)</signal>
+ <signal>sliderMoved(int)</signal>
<receiver>spinBoxSlice</receiver>
<slot>setValue(int)</slot>
<hints>
<hint type="sourcelabel">
- <x>364</x>
- <y>27</y>
+ <x>431</x>
+ <y>24</y>
</hint>
<hint type="destinationlabel">
<x>321</x>
- <y>29</y>
+ <y>20</y>
</hint>
</hints>
</connection>
@@ -260,12 +287,12 @@
<slot>setDisabled(bool)</slot>
<hints>
<hint type="sourcelabel">
- <x>761</x>
- <y>18</y>
+ <x>1065</x>
+ <y>22</y>
</hint>
<hint type="destinationlabel">
- <x>870</x>
- <y>14</y>
+ <x>1166</x>
+ <y>21</y>
</hint>
</hints>
</connection>
diff --git a/scripts/gui/phasemap_creator.py b/scripts/gui/phasemap_creator.py
index 9871cd6..3512897 100644
--- a/scripts/gui/phasemap_creator.py
+++ b/scripts/gui/phasemap_creator.py
@@ -11,192 +11,70 @@
import os
import sys
-import hyperspy.api as hs
+from PyQt4 import QtGui, QtCore
+from PyQt4.uic import loadUiType
-from pyramid import PhaseMap
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
import numpy as np
+import pyramid as pr
+import hyperspy.api as hs
from PIL import Image
-from PyQt4 import QtCore, QtGui
-from matplotlibwidget import MatplotlibWidget
-
-try:
- _fromUtf8 = QtCore.QString.fromUtf8
-except AttributeError:
- def _fromUtf8(s):
- return s
-
-try:
- _encoding = QtGui.QApplication.UnicodeUTF8
- def _translate(context, text, disambig):
- return QtGui.QApplication.translate(context, text, disambig, _encoding)
-except AttributeError:
+UI_MainWindow, QMainWindow = loadUiType('phasemap_creator.ui')
- def _translate(context, text, disambig):
- return QtGui.QApplication.translate(context, text, disambig)
+class Main(QMainWindow, UI_MainWindow):
-class UI_PhaseMapCreatorMain(QtGui.QWidget):
- def __init__(self, parent=None):
- QtGui.QWidget.__init__(self, parent)
- Form = self
- self.setGeometry(100, 100, 900, 900)
- self.setWindowTitle('PhaseMap Creator')
- Form.setObjectName(_fromUtf8('PhaseMap Creator'))
- ###########################################################################################
- self.verticalLayout = QtGui.QVBoxLayout(Form)
- self.verticalLayout.setObjectName(_fromUtf8("verticalLayout"))
- self.mplwidget = MatplotlibWidget(Form)
- self.mplwidget.setObjectName(_fromUtf8("mplwidget"))
- self.verticalLayout.addWidget(self.mplwidget)
- self.horizontalLayout = QtGui.QHBoxLayout()
- self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
- self.pushButton_phase = QtGui.QPushButton(Form)
- self.pushButton_phase.setObjectName(_fromUtf8("pushButton_phase"))
- self.horizontalLayout.addWidget(self.pushButton_phase)
- self.pushButton_mask = QtGui.QPushButton(Form)
- self.pushButton_mask.setObjectName(_fromUtf8("pushButton_mask"))
- self.horizontalLayout.addWidget(self.pushButton_mask)
- self.pushButton_conf = QtGui.QPushButton(Form)
- self.pushButton_conf.setObjectName(_fromUtf8("pushButton_conf"))
- self.horizontalLayout.addWidget(self.pushButton_conf)
- self.pushButton_export = QtGui.QPushButton(Form)
- self.pushButton_export.setObjectName(_fromUtf8("pushButton_export"))
- self.horizontalLayout.addWidget(self.pushButton_export)
- self.verticalLayout.addLayout(self.horizontalLayout)
- self.horizontalLayout_2 = QtGui.QHBoxLayout()
- self.horizontalLayout_2.setObjectName(_fromUtf8("horizontalLayout_2"))
- self.label_a = QtGui.QLabel(Form)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Preferred)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.label_a.sizePolicy().hasHeightForWidth())
- self.label_a.setSizePolicy(sizePolicy)
- self.label_a.setObjectName(_fromUtf8("label_a"))
- self.horizontalLayout_2.addWidget(self.label_a)
- self.doubleSpinBox_a = QtGui.QDoubleSpinBox(Form)
- self.doubleSpinBox_a.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignTrailing |
- QtCore.Qt.AlignVCenter)
- self.doubleSpinBox_a.setMaximum(1000)
- self.doubleSpinBox_a.setProperty("value", 1)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Fixed)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.doubleSpinBox_a.sizePolicy().hasHeightForWidth())
- self.doubleSpinBox_a.setSizePolicy(sizePolicy)
- self.doubleSpinBox_a.setObjectName(_fromUtf8("doubleSpinBox_a"))
- self.horizontalLayout_2.addWidget(self.doubleSpinBox_a)
- self.label_thres = QtGui.QLabel(Form)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Preferred)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.label_thres.sizePolicy().hasHeightForWidth())
- self.label_thres.setSizePolicy(sizePolicy)
- self.label_thres.setObjectName(_fromUtf8("label_thres"))
- self.horizontalLayout_2.addWidget(self.label_thres)
- self.doubleSpinBox_thres = QtGui.QDoubleSpinBox(Form)
- self.doubleSpinBox_thres.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignTrailing |
- QtCore.Qt.AlignVCenter)
- self.doubleSpinBox_thres.setMaximum(0)
- self.doubleSpinBox_thres.setProperty("value", 0)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Fixed)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.doubleSpinBox_thres.sizePolicy().hasHeightForWidth())
- self.doubleSpinBox_thres.setSizePolicy(sizePolicy)
- self.doubleSpinBox_thres.setObjectName(_fromUtf8("doubleSpinBox_thres"))
- self.horizontalLayout_2.addWidget(self.doubleSpinBox_thres)
- self.horizontalScrollBar = QtGui.QScrollBar(Form)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.MinimumExpanding, QtGui.QSizePolicy.Fixed)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.horizontalScrollBar.sizePolicy().hasHeightForWidth())
- self.horizontalScrollBar.setSizePolicy(sizePolicy)
- self.horizontalScrollBar.setOrientation(QtCore.Qt.Horizontal)
- self.horizontalScrollBar.setMaximum(0)
- self.horizontalScrollBar.setObjectName(_fromUtf8("horizontalScrollBar"))
- self.horizontalLayout_2.addWidget(self.horizontalScrollBar)
- self.checkBox_mask = QtGui.QCheckBox(Form)
- self.checkBox_mask.setChecked(True)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.checkBox_mask.sizePolicy().hasHeightForWidth())
- self.checkBox_mask.setSizePolicy(sizePolicy)
- self.checkBox_mask.setObjectName(_fromUtf8("checkBox_mask"))
- self.horizontalLayout_2.addWidget(self.checkBox_mask)
- self.checkBox_conf = QtGui.QCheckBox(Form)
- self.checkBox_conf.setChecked(True)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.checkBox_conf.sizePolicy().hasHeightForWidth())
- self.checkBox_conf.setSizePolicy(sizePolicy)
- self.checkBox_conf.setObjectName(_fromUtf8("checkBox_conf"))
- self.horizontalLayout_2.addWidget(self.checkBox_conf)
- self.verticalLayout.addLayout(self.horizontalLayout_2)
- ###########################################################################################
- self.retranslateUi(Form)
- # CONNECTS:
- self.connect(self.pushButton_phase, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ def __init__(self):
+ super().__init__()
+ self.setupUi(self)
+ self.connect(self.pushButton_phase, QtCore.SIGNAL('clicked()'),
self.load_phase)
- self.connect(self.pushButton_mask, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.connect(self.pushButton_mask, QtCore.SIGNAL('clicked()'),
self.load_mask)
- self.connect(self.pushButton_conf, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.connect(self.pushButton_conf, QtCore.SIGNAL('clicked()'),
self.load_conf)
- self.connect(self.pushButton_export, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.connect(self.pushButton_export, QtCore.SIGNAL('clicked()'),
self.export)
- self.connect(self.horizontalScrollBar, QtCore.SIGNAL(_fromUtf8("valueChanged(int)")),
+ self.connect(self.horizontalScrollBar, QtCore.SIGNAL('valueChanged(int)'),
self.doubleSpinBox_thres.setValue)
- self.connect(self.doubleSpinBox_thres, QtCore.SIGNAL(_fromUtf8("valueChanged(double)")),
+ self.connect(self.doubleSpinBox_thres, QtCore.SIGNAL('valueChanged(double)'),
self.horizontalScrollBar.setValue)
- self.connect(self.checkBox_mask, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.connect(self.checkBox_mask, QtCore.SIGNAL('clicked()'),
self.update_phasemap)
- self.connect(self.checkBox_conf, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.connect(self.checkBox_conf, QtCore.SIGNAL('clicked()'),
self.update_phasemap)
- self.connect(self.doubleSpinBox_a, QtCore.SIGNAL(_fromUtf8('editingFinished()')),
+ self.connect(self.doubleSpinBox_a, QtCore.SIGNAL('editingFinished()'),
self.update_phasemap)
- self.connect(self.doubleSpinBox_thres, QtCore.SIGNAL(_fromUtf8('valueChanged(double)')),
+ self.connect(self.doubleSpinBox_thres, QtCore.SIGNAL('valueChanged(double)'),
self.update_mask)
- QtCore.QMetaObject.connectSlotsByName(Form)
- # OTHER STUFF:
- self.mplwidget.axes.set_visible(False)
- self.mplwidget.axes.set_visible(False)
- self.mplwidget.axes.set_visible(False)
- self.pushButton_mask.setEnabled(False)
- self.pushButton_conf.setEnabled(False)
- self.pushButton_export.setEnabled(False)
- self.doubleSpinBox_thres.setEnabled(False)
- self.horizontalScrollBar.setEnabled(False)
self.phase_loaded = False
self.mask_loaded = False
- self.dir = ''
+ self.dir = os.path.join(pr.DIR_FILES)
- def retranslateUi(self, Form):
- ###########################################################################################
- Form.setWindowTitle(_translate("Form", "PhaseMap Creator", None))
- self.pushButton_phase.setText(_translate("Form", "Load Phase", None))
- self.pushButton_mask.setText(_translate("Form", "Load Mask", None))
- self.pushButton_conf.setText(_translate("Form", "Load Confidence", None))
- self.pushButton_export.setText(_translate("Form", "Export PhaseMap", None))
- self.label_a.setText(_translate("Form", "Grid Spacing [nm]:", None))
- self.label_thres.setText(_translate("Form", "Mask Threshold:", None))
- self.checkBox_mask.setText(_translate("Form", "show mask", None))
- self.checkBox_conf.setText(_translate("Form", "show confidence", None))
- ###########################################################################################
+ def addmpl(self):
+ fig = Figure()
+ fig.add_subplot(111, aspect='equal')
+ self.canvas = FigureCanvas(fig)
+ self.mplLayout.addWidget(self.canvas)
+ self.canvas.draw()
+ self.toolbar = NavigationToolbar(self.canvas, self, coordinates=True)
+ self.mplLayout.addWidget(self.toolbar)
def update_phasemap(self):
if self.phase_loaded:
self.phase_map.a = self.doubleSpinBox_a.value()
show_mask = self.checkBox_mask.isChecked()
show_conf = self.checkBox_conf.isChecked()
- self.mplwidget.axes.clear()
- self.mplwidget.axes.hold(True)
- self.phase_map.display_phase('PhaseMap', axis=self.mplwidget.axes,
+ self.canvas.figure.axes[0].clear()
+ self.canvas.figure.axes[0].hold(True)
+ self.phase_map.display_phase('PhaseMap', axis=self.canvas.figure.axes[0],
show_mask=show_mask, show_conf=show_conf, cbar=False)
- self.mplwidget.draw()
+ self.canvas.draw()
def update_mask(self):
if self.mask_loaded:
@@ -209,14 +87,13 @@ class UI_PhaseMapCreatorMain(QtGui.QWidget):
def load_phase(self):
try:
self.phase_path = QtGui.QFileDialog.getOpenFileName(self, 'Load Phase', self.dir)
- self.phase_map = PhaseMap.from_signal(hs.load(self.phase_path))
+ self.phase_map = pr.PhaseMap.from_signal(hs.load(self.phase_path))
except ValueError:
return # Abort if no phase_path is selected!
self.doubleSpinBox_a.setValue(self.phase_map.a)
self.dir = os.path.join(os.path.dirname(self.phase_path))
- self.mplwidget.axes.set_visible(True)
- self.mplwidget.axes.set_visible(True)
- self.mplwidget.axes.set_visible(True)
+ if not self.phase_loaded:
+ self.addmpl()
self.pushButton_mask.setEnabled(True)
self.pushButton_conf.setEnabled(True)
self.pushButton_export.setEnabled(True)
@@ -258,7 +135,7 @@ class UI_PhaseMapCreatorMain(QtGui.QWidget):
except ValueError:
return # Abort if no conf_path is selected!
confidence = hs.load(conf_path).data
- confidence /= confidence.max()
+ confidence = confidence / confidence.max()
confidence = np.asarray(Image.fromarray(confidence).resize(self.phase_map.dim_uv))
self.phase_map.confidence = confidence
self.update_phasemap()
@@ -276,6 +153,6 @@ class UI_PhaseMapCreatorMain(QtGui.QWidget):
if __name__ == '__main__':
app = QtGui.QApplication(sys.argv)
- widget = UI_PhaseMapCreatorMain()
- widget.show()
+ main = Main()
+ main.show()
sys.exit(app.exec_())
diff --git a/scripts/gui/phasemap_creator.ui b/scripts/gui/phasemap_creator.ui
index 80c7391..caa64fc 100644
--- a/scripts/gui/phasemap_creator.ui
+++ b/scripts/gui/phasemap_creator.ui
@@ -1,209 +1,222 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
- <class>Form</class>
- <widget class="QWidget" name="Form">
+ <class>MainWindow</class>
+ <widget class="QMainWindow" name="MainWindow">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
- <width>789</width>
- <height>775</height>
+ <width>726</width>
+ <height>632</height>
</rect>
</property>
<property name="windowTitle">
- <string>Form</string>
+ <string>MainWindow</string>
</property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="MatplotlibWidget" name="mplwidget"/>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QPushButton" name="pushButton_phase">
- <property name="text">
- <string>Load Phase</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_mask">
- <property name="text">
- <string>Load Mask</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_conf">
- <property name="text">
- <string>Load Confidence</string>
- </property>
- <property name="checkable">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_export">
- <property name="text">
- <string>Export Phasemap</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>Grid spacing [nm]:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="doubleSpinBox_2">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>60</width>
- <height>0</height>
- </size>
- </property>
- <property name="baseSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="alignment">
- <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
- </property>
- <property name="maximum">
- <double>1000.000000000000000</double>
- </property>
- <property name="value">
- <double>1.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Mask Threshold:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="doubleSpinBox">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>60</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="baseSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="alignment">
- <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
- </property>
- <property name="prefix">
- <string/>
- </property>
- <property name="decimals">
- <number>2</number>
- </property>
- <property name="maximum">
- <double>0.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QScrollBar" name="horizontalScrollBar">
- <property name="sizePolicy">
- <sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="maximum">
- <number>0</number>
- </property>
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBox_mask">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>show mask</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBox_conf">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>show confidence</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
+ <widget class="QWidget" name="centralwidget">
+ <property name="windowTitle">
+ <string>Form</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <widget class="QWidget" name="mplwidget" native="true">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_2">
+ <item>
+ <layout class="QVBoxLayout" name="mplLayout"/>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout">
+ <item>
+ <widget class="QPushButton" name="pushButton_phase">
+ <property name="text">
+ <string>Load Phase</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_mask">
+ <property name="text">
+ <string>Load Mask</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_conf">
+ <property name="text">
+ <string>Load Confidence</string>
+ </property>
+ <property name="checkable">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_export">
+ <property name="text">
+ <string>Export Phasemap</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_2">
+ <item>
+ <widget class="QLabel" name="label_2">
+ <property name="text">
+ <string>Grid spacing [nm]:</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QDoubleSpinBox" name="doubleSpinBox_a">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>60</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="baseSize">
+ <size>
+ <width>0</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
+ </property>
+ <property name="maximum">
+ <double>1000.000000000000000</double>
+ </property>
+ <property name="value">
+ <double>1.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>Mask Threshold:</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QDoubleSpinBox" name="doubleSpinBox_thres">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>60</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>16777215</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="baseSize">
+ <size>
+ <width>0</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
+ </property>
+ <property name="prefix">
+ <string/>
+ </property>
+ <property name="decimals">
+ <number>2</number>
+ </property>
+ <property name="maximum">
+ <double>0.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QScrollBar" name="horizontalScrollBar">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="maximum">
+ <number>0</number>
+ </property>
+ <property name="singleStep">
+ <number>1</number>
+ </property>
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="checkBox_mask">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>show mask</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="checkBox_conf">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>show confidence</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
</widget>
- <customwidgets>
- <customwidget>
- <class>MatplotlibWidget</class>
- <extends>QWidget</extends>
- <header>matplotlibwidget</header>
- </customwidget>
- </customwidgets>
<resources/>
<connections/>
</ui>
diff --git a/scripts/magdata/magdata_from_vtk.py b/scripts/magdata/magdata_from_vtk.py
index d16a223..b17b8e7 100644
--- a/scripts/magdata/magdata_from_vtk.py
+++ b/scripts/magdata/magdata_from_vtk.py
@@ -1,8 +1,6 @@
# -*- coding: utf-8 -*-
"""Create magnetization distributions from vtk-files."""
-from __future__ import print_function
-
import logging.config
import os
from time import sleep
@@ -25,8 +23,7 @@ b_0 = 1.
def enclosing_zero(x, y, nx=30, ny=30):
- """
- Construct a grid of points, that are some distance away from points (x, y)
+ """Construct a grid of points, that are some distance away from points (x, y)
Parameters
----------
@@ -47,7 +44,7 @@ def enclosing_zero(x, y, nx=30, ny=30):
dx = x.ptp() / nx
dy = y.ptp() / ny
xp, yp = np.mgrid[x.min() - 2 * dx:x.max() + 2 * dx:(nx + 2) * 1j,
- y.min() - 2 * dy:y.max() + 2 * dy:(ny + 2) * 1j]
+ y.min() - 2 * dy:y.max() + 2 * dy:(ny + 2) * 1j]
xp = xp.ravel()
yp = yp.ravel()
# Use KDTree to answer the question: "which point of set (x, y) is the
diff --git a/scripts/phasemap/phasemap_from_dm3.py b/scripts/phasemap/phasemap_from_dm3.py
index 3eaf9d6..0301697 100644
--- a/scripts/phasemap/phasemap_from_dm3.py
+++ b/scripts/phasemap/phasemap_from_dm3.py
@@ -7,18 +7,19 @@ import os
import numpy as np
from PIL import Image
-import hyperspy.hspy as hp
-import pyramid as py
+import hyperspy.api as hs
+import pyramid as pr
import matplotlib.pyplot as plt
-logging.config.fileConfig(py.LOGGING_CONFIG, disable_existing_loggers=False)
+logging.config.fileConfig(pr.LOGGING_CONFIG, disable_existing_loggers=False)
###################################################################################################
-path_mag = 'zi_an_38kx_220K_09p32_w1198_h154.dm3'
-path_mask = 'zi_an_38kx_220K_00p10_w1198_h154_mask_in.txt'
+path_mag = 'zi_an_skyrmions_02_38kx_220K_06p27_r_t_magn_x13_y27_w420_h400.dm3'
+path_mask = 'zi_an_skyrmions_02_38kx_220K_06p27_r_t_magn_x13_y27_w420_h400_mask_roi.txt'
path_conf = None
-filename = 'phasemap_dm3_zi_an_magnetite_09p32.hdf5'
+filename = 'phasemap_dm3_{}.hdf5'.format(os.path.splitext(path_mag)[0])
+print(filename)
a = 1.
dim_uv = None
threshold = 0.5
@@ -26,16 +27,16 @@ flip_up_down = True
###################################################################################################
# Load images:
-im_mag_hp = hp.load(os.path.join(py.DIR_FILES, 'dm3', path_mag))
+im_mag_hp = hs.load(os.path.join(pr.DIR_FILES, 'dm3', path_mag))
im_mag = Image.fromarray(im_mag_hp.data)
if path_mask is not None:
# im_mask_hp = hp.load(os.path.join(pr.DIR_FILES, 'dm3', path_mask))
- mask_data = np.genfromtxt(os.path.join(py.DIR_FILES, 'dm3', path_mask), delimiter=',')
+ mask_data = np.genfromtxt(os.path.join(pr.DIR_FILES, 'dm3', path_mask), delimiter=',')
im_mask = Image.fromarray(mask_data) # )im_mask_hp.data)
else:
im_mask = Image.new('F', im_mag.size, 'white')
if path_conf is not None:
- im_conf_hp = hp.load(os.path.join(py.DIR_FILES, 'dm3', path_conf))
+ im_conf_hp = hs.load(os.path.join(pr.DIR_FILES, 'dm3', path_conf))
im_conf = Image.fromarray(im_conf_hp.data)
else:
im_conf = Image.new('F', im_mag.size, 'white')
@@ -54,7 +55,7 @@ mask = np.where(np.asarray(im_mask) >= threshold, True, False)
confidence = np.where(np.asarray(im_conf) >= threshold, 1, 0)
# Create and save PhaseMap object:
-phase_map = py.PhaseMap(a, phase, mask, confidence, unit='rad')
-phase_map.save_to_hdf5(os.path.join(py.DIR_FILES, 'phasemap', filename), overwrite=True)
+phase_map = pr.PhaseMap(a, phase, mask, confidence, unit='rad')
+phase_map.save_to_hdf5(os.path.join(pr.DIR_FILES, 'phasemap', filename), overwrite=True)
phase_map.display_combined()
plt.show()
diff --git a/scripts/phasemap/phasemap_from_raw.py b/scripts/phasemap/phasemap_from_raw.py
index 8870041..71cca7d 100644
--- a/scripts/phasemap/phasemap_from_raw.py
+++ b/scripts/phasemap/phasemap_from_raw.py
@@ -4,12 +4,11 @@
import logging.config
import os
-import pyramid as pr
-
import matplotlib.pyplot as plt
import numpy as np
from PIL import Image
+import pyramid as pr
logging.config.fileConfig(pr.LOGGING_CONFIG, disable_existing_loggers=False)
diff --git a/scripts/reconstruction/reconstruction_2d_from_phasemap.py b/scripts/reconstruction/reconstruction_2d_from_phasemap.py
index 7ed9b37..7d04d2c 100644
--- a/scripts/reconstruction/reconstruction_2d_from_phasemap.py
+++ b/scripts/reconstruction/reconstruction_2d_from_phasemap.py
@@ -1,19 +1,20 @@
# -*- coding: utf-8 -*-
"""Reconstruct a magnetization distributions from a single phase map."""
-from __future__ import print_function
+import logging.config
+import matplotlib.pyplot as plt
import numpy as np
+
import pyramid as pr
from jutil.taketime import TakeTime
-import logging.config
logging.config.fileConfig(pr.LOGGING_CONFIG, disable_existing_loggers=False)
###################################################################################################
-phase_name = 'phasemap_gui_150917_skyrm_M_100mT'
+phase_name = 'phasemap_dm3_zi_an_skyrmions_02_38kx_220K_06p27_r_t_magn_x13_y27_w420_h400'
b_0 = 1 # in T
-lam = 1E-1
+lam = 1E-3
max_iter = 100
buffer_pixel = 0
order = 1
@@ -47,7 +48,6 @@ else:
mag_data_buffer = mag_data_rec.copy()
mag_data_rec.crop((0, buffer_pixel, buffer_pixel))
mag_name = '{}_lam={}'.format(phase_name.replace('phasemap', 'magdata_rec'), lam)
-mag_data_rec = mag_data_rec.flip(axis='y')
mag_data_rec.save_to_hdf5(mag_name + '.hdf5', overwrite=True)
# Plot stuff:
@@ -69,3 +69,4 @@ difference = (phase_map_rec.phase - phase_map.phase).mean()
(phase_map_rec - phase_map).display_phase('Difference (mean: {:.2g})'.format(difference))
if order is not None:
fwd_model.ramp(0).display_combined('Fitted Ramp')
+plt.show()
diff --git a/setup.py b/setup.py
index 3d455d0..d2b588f 100644
--- a/setup.py
+++ b/setup.py
@@ -2,8 +2,6 @@
# coding=utf-8
"""Setup for testing, building, distributing and installing the 'Pyramid'-package"""
-from __future__ import print_function
-
import os
import re
import subprocess
@@ -16,7 +14,7 @@ from setuptools import setup, find_packages
from setuptools.extension import Extension
# Import Hyperspy before actually doing stuff, to set the PyQT API at the very beginning (to 2).
-# If this is not done, something sets it to 1 befor HyperSpy is imported, which leads to errors.
+# If this is not done, something sets it to 1 befor Hyperspy is imported, which leads to errors.
DISTNAME = 'pyramid'
@@ -104,9 +102,9 @@ def write_version_py(filename='pyramid/version.py'):
"""
version_string = '# -*- coding: utf-8 -*-\n' + \
- '"""This file is generated automatically by the Pyramid `setup.py`"""\n' + \
- 'version = \'{}\'\n'.format(VERSION) + \
- 'hg_revision = \'{}\'\n'.format(hg_version())
+ '""""This file is generated automatically by the Pyramid `setup.py`"""\n' + \
+ 'version = "{}"\n'.format(VERSION) + \
+ 'hg_revision = "{}"\n'.format(hg_version())
with open(os.path.join(os.path.dirname(__file__), filename), 'w') as vfile:
vfile.write(version_string)
@@ -148,16 +146,12 @@ setup(name=DISTNAME,
version=VERSION,
packages=find_packages(exclude=['tests']),
include_dirs=[numpy.get_include()],
- requires=['numpy', 'matplotlib', 'mayavi', 'hyperspy', 'PIL', 'scipy', 'pyfftw', 'Cython'],
+ requires=['numpy', 'scipy', 'matplotlib', 'Pillow',
+ 'mayavi', 'pyfftw', 'hyperspy', 'Cython'],
scripts=get_files('scripts'),
test_suite='nose.collector',
cmdclass={'build_ext': build_ext, 'build': build},
ext_package='pyramid/numcore',
- ext_modules=[
- Extension('phasemapper_core', ['pyramid/numcore/phasemapper_core.pyx'],
- include_dirs=[numpy.get_include()],
- extra_compile_args=['-march=native', '-mtune=native']
- )
- ]
- )
+ ext_modules=[Extension('phasemapper_core', ['pyramid/numcore/phasemapper_core.pyx'],
+ include_dirs=[numpy.get_include()])])
print('-------------------------------------------------------------------------------\n')
--
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