From 2cf27a5aee85d9a00a63731eebb9c4a46b03e6c8 Mon Sep 17 00:00:00 2001
From: Stephane Dallongeville <stephane.dallongeville@pasteur.fr>
Date: Thu, 21 Jul 2022 16:24:14 +0200
Subject: [PATCH] Initial commit
---
LICENSE.md | 595 ++++++++++++++++++
pom.xml | 83 +++
.../ylemontag/matlabimporter/MainPanel.java | 270 ++++++++
.../matlabimporter/MatlabImporterPlugin.java | 332 ++++++++++
.../matlabimporter/VariableListComponent.java | 129 ++++
.../resources/icon-Matlab-function-caller.png | Bin 0 -> 4052 bytes
.../tooltip-Matlab-function-caller.png | Bin 0 -> 21881 bytes
7 files changed, 1409 insertions(+)
create mode 100644 LICENSE.md
create mode 100644 pom.xml
create mode 100644 src/main/java/plugins/ylemontag/matlabimporter/MainPanel.java
create mode 100644 src/main/java/plugins/ylemontag/matlabimporter/MatlabImporterPlugin.java
create mode 100644 src/main/java/plugins/ylemontag/matlabimporter/VariableListComponent.java
create mode 100644 src/main/resources/icon-Matlab-function-caller.png
create mode 100644 src/main/resources/tooltip-Matlab-function-caller.png
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..bf09192
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,595 @@
+GNU General Public License
+==========================
+
+_Version 3, 29 June 2007_
+_Copyright (C) 2007 Free Software Foundation, Inc. <<http://fsf.org/>>_
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+## Preamble
+
+The GNU General Public License is a free, copyleft license for software and other
+kinds of works.
+
+The licenses for most software and other practical works are designed to take away
+your freedom to share and change the works. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change all versions of a
+program--to make sure it remains free software for all its users. We, the Free
+Software Foundation, use the GNU General Public License for most of our software; it
+applies also to any other work released this way by its authors. You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our General
+Public Licenses are designed to make sure that you have the freedom to distribute
+copies of free software (and charge for them if you wish), that you receive source
+code or can get it if you want it, that you can change the software or use pieces of
+it in new free programs, and that you know you can do these things.
+
+To protect your rights, we need to prevent others from denying you these rights or
+asking you to surrender the rights. Therefore, you have certain responsibilities if
+you distribute copies of the software, or if you modify it: responsibilities to
+respect the freedom of others.
+
+For example, if you distribute copies of such a program, whether gratis or for a fee,
+you must pass on to the recipients the same freedoms that you received. You must make
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+
+Developers that use the GNU GPL protect your rights with two steps: **(1)** assert
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+
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+requires that modified versions be marked as changed, so that their problems will not
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+Some devices are designed to deny users access to install or run modified versions of
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+
+Finally, every program is threatened constantly by software patents. States should
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+
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+
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+You may convey verbatim copies of the Program's source code as you receive it, in any
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+A compilation of a covered work with other separate and independent works, which are
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+copyright are not used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit. Inclusion of a covered work in an aggregate
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+
+### 6. Conveying Non-Source Forms
+
+You may convey a covered work in object code form under the terms of sections 4 and
+5, provided that you also convey the machine-readable Corresponding Source under the
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+* **a)** Convey the object code in, or embodied in, a physical product (including a
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+three years and valid for as long as you offer spare parts or customer support for
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+Corresponding Source as a System Library, need not be included in conveying the
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+A "User Product" is either **(1)** a "consumer product", which
+means any tangible personal property which is normally used for personal, family, or
+household purposes, or **(2)** anything designed or sold for incorporation into a
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+functioning of the modified object code is in no case prevented or interfered with
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+If you convey an object code work under this section in, or with, or specifically for
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+
+### 7. Additional Terms
+
+"Additional permissions" are terms that supplement the terms of this
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+were included in this License, to the extent that they are valid under applicable
+law. If additional permissions apply only to part of the Program, that part may be
+used separately under those permissions, but the entire Program remains governed by
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+
+When you convey a copy of a covered work, you may at your option remove any
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+Additional terms, permissive or non-permissive, may be stated in the form of a
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+
+### 8. Termination
+
+You may not propagate or modify a covered work except as expressly provided under
+this License. Any attempt otherwise to propagate or modify it is void, and will
+automatically terminate your rights under this License (including any patent licenses
+granted under the third paragraph of section 11).
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+However, if you cease all violation of this License, then your license from a
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+copyright holder explicitly and finally terminates your license, and **(b)** permanently,
+if the copyright holder fails to notify you of the violation by some reasonable means
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+Moreover, your license from a particular copyright holder is reinstated permanently
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+
+### 9. Acceptance Not Required for Having Copies
+
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+
+### 10. Automatic Licensing of Downstream Recipients
+
+Each time you convey a covered work, the recipient automatically receives a license
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+that any patent claim is infringed by making, using, selling, offering for sale, or
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+
+### 11. Patents
+
+A "contributor" is a copyright holder who authorizes use under this
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+
+A contributor's "essential patent claims" are all patent claims owned or
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+
+Each contributor grants you a non-exclusive, worldwide, royalty-free patent license
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+express permission to practice a patent or covenant not to sue for patent
+infringement). To "grant" such a patent license to a party means to make
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+
+If you convey a covered work, knowingly relying on a patent license, and the
+Corresponding Source of the work is not available for anyone to copy, free of charge
+and under the terms of this License, through a publicly available network server or
+other readily accessible means, then you must either **(1)** cause the Corresponding
+Source to be so available, or **(2)** arrange to deprive yourself of the benefit of the
+patent license for this particular work, or **(3)** arrange, in a manner consistent with
+the requirements of this License, to extend the patent license to downstream
+recipients. "Knowingly relying" means you have actual knowledge that, but
+for the patent license, your conveying the covered work in a country, or your
+recipient's use of the covered work in a country, would infringe one or more
+identifiable patents in that country that you have reason to believe are valid.
+
+If, pursuant to or in connection with a single transaction or arrangement, you
+convey, or propagate by procuring conveyance of, a covered work, and grant a patent
+license to some of the parties receiving the covered work authorizing them to use,
+propagate, modify or convey a specific copy of the covered work, then the patent
+license you grant is automatically extended to all recipients of the covered work and
+works based on it.
+
+A patent license is "discriminatory" if it does not include within the
+scope of its coverage, prohibits the exercise of, or is conditioned on the
+non-exercise of one or more of the rights that are specifically granted under this
+License. You may not convey a covered work if you are a party to an arrangement with
+a third party that is in the business of distributing software, under which you make
+payment to the third party based on the extent of your activity of conveying the
+work, and under which the third party grants, to any of the parties who would receive
+the covered work from you, a discriminatory patent license **(a)** in connection with
+copies of the covered work conveyed by you (or copies made from those copies), or **(b)**
+primarily for and in connection with specific products or compilations that contain
+the covered work, unless you entered into that arrangement, or that patent license
+was granted, prior to 28 March 2007.
+
+Nothing in this License shall be construed as excluding or limiting any implied
+license or other defenses to infringement that may otherwise be available to you
+under applicable patent law.
+
+### 12. No Surrender of Others' Freedom
+
+If conditions are imposed on you (whether by court order, agreement or otherwise)
+that contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot convey a covered work so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not convey it at all. For example, if you
+agree to terms that obligate you to collect a royalty for further conveying from
+those to whom you convey the Program, the only way you could satisfy both those terms
+and this License would be to refrain entirely from conveying the Program.
+
+### 13. Use with the GNU Affero General Public License
+
+Notwithstanding any other provision of this License, you have permission to link or
+combine any covered work with a work licensed under version 3 of the GNU Affero
+General Public License into a single combined work, and to convey the resulting work.
+The terms of this License will continue to apply to the part which is the covered
+work, but the special requirements of the GNU Affero General Public License, section
+13, concerning interaction through a network will apply to the combination as such.
+
+### 14. Revised Versions of this License
+
+The Free Software Foundation may publish revised and/or new versions of the GNU
+General Public License from time to time. Such new versions will be similar in spirit
+to the present version, but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program specifies that
+a certain numbered version of the GNU General Public License "or any later
+version" applies to it, you have the option of following the terms and
+conditions either of that numbered version or of any later version published by the
+Free Software Foundation. If the Program does not specify a version number of the GNU
+General Public License, you may choose any version ever published by the Free
+Software Foundation.
+
+If the Program specifies that a proxy can decide which future versions of the GNU
+General Public License can be used, that proxy's public statement of acceptance of a
+version permanently authorizes you to choose that version for the Program.
+
+Later license versions may give you additional or different permissions. However, no
+additional obligations are imposed on any author or copyright holder as a result of
+your choosing to follow a later version.
+
+### 15. Disclaimer of Warranty
+
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
+EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
+EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE
+QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
+DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+### 16. Limitation of Liability
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY
+COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS
+PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL,
+INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE
+OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE
+WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+### 17. Interpretation of Sections 15 and 16
+
+If the disclaimer of warranty and limitation of liability provided above cannot be
+given local legal effect according to their terms, reviewing courts shall apply local
+law that most closely approximates an absolute waiver of all civil liability in
+connection with the Program, unless a warranty or assumption of liability accompanies
+a copy of the Program in return for a fee.
+
+_END OF TERMS AND CONDITIONS_
+
+## How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible use to
+the public, the best way to achieve this is to make it free software which everyone
+can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach them
+to the start of each source file to most effectively state the exclusion of warranty;
+and each file should have at least the "copyright" line and a pointer to
+where the full notice is found.
+
+ Apache Commons Codec - Icy plugin (http://icy.bioimageanalysis.org/).
+ Copyright (C) 2021 Biological Image Analysis unit, Institut Pasteur
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program does terminal interaction, make it output a short notice like this
+when it starts in an interactive mode:
+
+ Apache Commons Codec Copyright (C) 2021 Biological Image Analysis unit, Institut Pasteur
+ This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type 'show c' for details.
+
+The hypothetical commands `show w` and `show c` should show the appropriate parts of
+the General Public License. Of course, your program's commands might be different;
+for a GUI interface, you would use an "about box".
+
+You should also get your employer (if you work as a programmer) or school, if any, to
+sign a "copyright disclaimer" for the program, if necessary. For more
+information on this, and how to apply and follow the GNU GPL, see
+<<http://www.gnu.org/licenses/>>.
+
+The GNU General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may consider it
+more useful to permit linking proprietary applications with the library. If this is
+what you want to do, use the GNU Lesser General Public License instead of this
+License. But first, please read
+<<http://www.gnu.org/philosophy/why-not-lgpl.html>>.
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..779acdf
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,83 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <!-- Inherited Icy Parent POM -->
+ <parent>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>parent-pom-plugin</artifactId>
+ <version>1.0.6</version>
+ </parent>
+
+ <!-- Project Information -->
+ <artifactId>matlab-importer</artifactId>
+ <version>2.5.1</version>
+
+ <packaging>jar</packaging>
+
+ <name>Matlab Importer</name>
+ <description>Import Matlab *.mat files as sequences in Icy.</description>
+ <inceptionYear>2022</inceptionYear>
+
+ <organization>
+ <name>Institut Pasteur</name>
+ <url>https://pasteur.fr</url>
+ </organization>
+
+ <licenses>
+ <license>
+ <name>GNU GPLv3</name>
+ <url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
+ <distribution>repo</distribution>
+ </license>
+ </licenses>
+
+ <developers>
+ <developer>
+ <id>ylemontag</id>
+ <name>Yoann Le Montagner</name>
+ <url>https://icy.bioimageanalysis.org/author/ylemontag/</url>
+ <roles>
+ <role>developer</role>
+ <role>maintainer</role>
+ </roles>
+ </developer>
+ </developers>
+
+ <!-- Project properties -->
+ <properties>
+
+ </properties>
+
+ <!-- Project build configuration -->
+ <build>
+ <plugins>
+ </plugins>
+ </build>
+
+ <!-- List of project's dependencies -->
+ <dependencies>
+ <!-- The core of Icy -->
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>icy-kernel</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>matlab-io</artifactId>
+ <version>2.5.2</version>
+ </dependency>
+ </dependencies>
+
+ <!-- Icy Maven repository (to find parent POM) -->
+ <repositories>
+ <repository>
+ <id>icy</id>
+ <name>Icy's Nexus</name>
+ <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ </repository>
+ </repositories>
+</project>
diff --git a/src/main/java/plugins/ylemontag/matlabimporter/MainPanel.java b/src/main/java/plugins/ylemontag/matlabimporter/MainPanel.java
new file mode 100644
index 0000000..19bfe08
--- /dev/null
+++ b/src/main/java/plugins/ylemontag/matlabimporter/MainPanel.java
@@ -0,0 +1,270 @@
+package plugins.ylemontag.matlabimporter;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.EtchedBorder;
+import javax.swing.filechooser.FileNameExtensionFilter;
+
+import plugins.ylemontag.matlabio.gui.ComplexModeComponent;
+import plugins.ylemontag.matlabio.gui.DimensionMappingComponent;
+import plugins.ylemontag.matlabio.gui.FileChooserComponent;
+
+public class MainPanel extends JPanel {
+
+ private static final long serialVersionUID = 1L;
+ private FileChooserComponent _fileChooserComponent;
+ private DimensionMappingComponent _dimensionMappingComponent;
+ private VariableListComponent _variableListComponent;
+ private JButton _actionButton;
+ private JCheckBox _doPrefixComponent;
+ private ComplexModeComponent _complexModeComponent;
+ private JButton _refreshButton;
+
+ /**
+ * Matlab file chooser component
+ */
+ public FileChooserComponent getFileComponent() {
+ return _fileChooserComponent;
+ }
+
+ /**
+ * Dimension mapping component
+ */
+ public DimensionMappingComponent getDimensionMappingComponent() {
+ return _dimensionMappingComponent;
+ }
+
+ /**
+ * Complex mode component
+ */
+ public ComplexModeComponent getComplexModeComponent() {
+ return _complexModeComponent;
+ }
+
+ /**
+ * Variable list component
+ */
+ public VariableListComponent getVariableComponent() {
+ return _variableListComponent;
+ }
+
+ /**
+ * Prefix check-box
+ */
+ public JCheckBox getDoPrefixComponent() {
+ return _doPrefixComponent;
+ }
+
+ /**
+ * Refresh button
+ */
+ public JButton getRefreshButton() {
+ return _refreshButton;
+ }
+
+ /**
+ * Action button
+ */
+ public JButton getActionButton() {
+ return _actionButton;
+ }
+
+ /**
+ * Create the panel
+ */
+ public MainPanel() {
+ setBorder(new EmptyBorder(5, 5, 5, 5));
+ setLayout(new BorderLayout(0, 0));
+
+ JPanel panel_8 = new JPanel();
+ add(panel_8, BorderLayout.SOUTH);
+ panel_8.setLayout(new BorderLayout(0, 0));
+
+ Component verticalStrut_1 = Box.createVerticalStrut(5);
+ panel_8.add(verticalStrut_1, BorderLayout.NORTH);
+
+ JPanel panel_9 = new JPanel();
+ panel_8.add(panel_9, BorderLayout.EAST);
+ panel_9.setLayout(new BoxLayout(panel_9, BoxLayout.X_AXIS));
+
+ Component horizontalStrut_1 = Box.createHorizontalStrut(5);
+ panel_9.add(horizontalStrut_1);
+
+ _refreshButton = new JButton("Refresh");
+ _refreshButton.setToolTipText("Refresh the list of variables");
+ panel_9.add(_refreshButton);
+
+ Component horizontalStrut_9 = Box.createHorizontalStrut(5);
+ panel_9.add(horizontalStrut_9);
+
+ _actionButton = new JButton("Import");
+ _actionButton.setToolTipText("Import the selected objects");
+ panel_9.add(_actionButton);
+
+ Component horizontalGlue_2 = Box.createHorizontalGlue();
+ panel_8.add(horizontalGlue_2, BorderLayout.CENTER);
+
+ _doPrefixComponent = new JCheckBox("Prefix with filename");
+ _doPrefixComponent.setToolTipText("The name of the imported sequences will be prefixed with the name of the Matlab .mat file");
+ panel_8.add(_doPrefixComponent, BorderLayout.WEST);
+
+ _variableListComponent = new VariableListComponent();
+
+ JScrollPane scrollPane = new JScrollPane(_variableListComponent);
+ add(scrollPane, BorderLayout.CENTER);
+
+ JPanel panel = new JPanel();
+ add(panel, BorderLayout.NORTH);
+ panel.setLayout(new BorderLayout(0, 0));
+
+ JPanel panel_1 = new JPanel();
+ panel.add(panel_1, BorderLayout.NORTH);
+ panel_1.setLayout(new BorderLayout(0, 0));
+
+ Component verticalStrut = Box.createVerticalStrut(5);
+ panel_1.add(verticalStrut, BorderLayout.SOUTH);
+
+ JPanel panel_4 = new JPanel();
+ panel_1.add(panel_4, BorderLayout.CENTER);
+ panel_4.setBorder(new EtchedBorder(EtchedBorder.LOWERED, null, null));
+ panel_4.setLayout(new BorderLayout(0, 0));
+
+ Component verticalStrut_5 = Box.createVerticalStrut(5);
+ panel_4.add(verticalStrut_5, BorderLayout.NORTH);
+
+ Component verticalStrut_6 = Box.createVerticalStrut(5);
+ panel_4.add(verticalStrut_6, BorderLayout.SOUTH);
+
+ Component horizontalStrut_4 = Box.createHorizontalStrut(5);
+ panel_4.add(horizontalStrut_4, BorderLayout.EAST);
+
+ JPanel panel_5 = new JPanel();
+ panel_4.add(panel_5, BorderLayout.CENTER);
+ panel_5.setLayout(new BoxLayout(panel_5, BoxLayout.Y_AXIS));
+
+ JPanel panel_7 = new JPanel();
+ panel_5.add(panel_7);
+ panel_7.setLayout(new BoxLayout(panel_7, BoxLayout.X_AXIS));
+
+ JLabel lblNewLabel = new JLabel("Source file");
+ panel_7.add(lblNewLabel);
+
+ Component horizontalGlue = Box.createHorizontalGlue();
+ panel_7.add(horizontalGlue);
+
+ Component verticalStrut_2 = Box.createVerticalStrut(5);
+ panel_5.add(verticalStrut_2);
+
+ JPanel panel_6 = new JPanel();
+ panel_5.add(panel_6);
+ panel_6.setLayout(new BorderLayout(0, 0));
+
+ FileNameExtensionFilter filter = new FileNameExtensionFilter("Matlab object files (*.mat)", "mat");
+ _fileChooserComponent = new FileChooserComponent(FileChooserComponent.Mode.OPEN_DIALOG, filter);
+ panel_6.add(_fileChooserComponent);
+
+ Component horizontalStrut_5 = Box.createHorizontalStrut(5);
+ panel_4.add(horizontalStrut_5, BorderLayout.WEST);
+
+ JPanel panel_2 = new JPanel();
+ panel_1.add(panel_2, BorderLayout.EAST);
+ panel_2.setLayout(new BoxLayout(panel_2, BoxLayout.X_AXIS));
+
+ Component horizontalStrut = Box.createHorizontalStrut(5);
+ panel_2.add(horizontalStrut);
+
+ JPanel panel_3 = new JPanel();
+ panel_2.add(panel_3);
+ panel_3.setBorder(new EtchedBorder(EtchedBorder.LOWERED, null, null));
+ panel_3.setLayout(new BorderLayout(0, 0));
+
+ Component verticalStrut_3 = Box.createVerticalStrut(5);
+ panel_3.add(verticalStrut_3, BorderLayout.NORTH);
+
+ Component verticalStrut_4 = Box.createVerticalStrut(5);
+ panel_3.add(verticalStrut_4, BorderLayout.SOUTH);
+
+ Component horizontalStrut_2 = Box.createHorizontalStrut(5);
+ panel_3.add(horizontalStrut_2, BorderLayout.WEST);
+
+ Component horizontalStrut_3 = Box.createHorizontalStrut(5);
+ panel_3.add(horizontalStrut_3, BorderLayout.EAST);
+
+ JPanel panel_10 = new JPanel();
+ panel_3.add(panel_10, BorderLayout.CENTER);
+ panel_10.setLayout(new BoxLayout(panel_10, BoxLayout.Y_AXIS));
+
+ JPanel panel_12 = new JPanel();
+ panel_10.add(panel_12);
+ panel_12.setLayout(new BoxLayout(panel_12, BoxLayout.X_AXIS));
+
+ JLabel lblNewLabel_1 = new JLabel("Dimension mapping");
+ panel_12.add(lblNewLabel_1);
+
+ Component horizontalGlue_1 = Box.createHorizontalGlue();
+ panel_12.add(horizontalGlue_1);
+
+ Component verticalStrut_7 = Box.createVerticalStrut(5);
+ panel_10.add(verticalStrut_7);
+
+ JPanel panel_11 = new JPanel();
+ panel_10.add(panel_11);
+ panel_11.setLayout(new BorderLayout(0, 0));
+
+ _dimensionMappingComponent = new DimensionMappingComponent();
+ _dimensionMappingComponent.setToolTipText("Describe how a multi-dimension Matlab array should be interpreted as a sequence");
+ panel_11.add(_dimensionMappingComponent, BorderLayout.CENTER);
+
+ Component horizontalStrut_6 = Box.createHorizontalStrut(5);
+ panel_2.add(horizontalStrut_6);
+
+ JPanel panel_13 = new JPanel();
+ panel_13.setBorder(new EtchedBorder(EtchedBorder.LOWERED, null, null));
+ panel_2.add(panel_13);
+ panel_13.setLayout(new BorderLayout(0, 0));
+
+ Component horizontalStrut_7 = Box.createHorizontalStrut(5);
+ panel_13.add(horizontalStrut_7, BorderLayout.WEST);
+
+ Component horizontalStrut_8 = Box.createHorizontalStrut(5);
+ panel_13.add(horizontalStrut_8, BorderLayout.EAST);
+
+ Component verticalStrut_8 = Box.createVerticalStrut(5);
+ panel_13.add(verticalStrut_8, BorderLayout.NORTH);
+
+ Component verticalStrut_9 = Box.createVerticalStrut(5);
+ panel_13.add(verticalStrut_9, BorderLayout.SOUTH);
+
+ JPanel panel_14 = new JPanel();
+ panel_13.add(panel_14, BorderLayout.CENTER);
+ panel_14.setLayout(new BoxLayout(panel_14, BoxLayout.Y_AXIS));
+
+ JPanel panel_15 = new JPanel();
+ panel_14.add(panel_15);
+ panel_15.setLayout(new BoxLayout(panel_15, BoxLayout.X_AXIS));
+
+ JLabel lblNewLabel_2 = new JLabel("Complex variables");
+ panel_15.add(lblNewLabel_2);
+
+ Component horizontalGlue_3 = Box.createHorizontalGlue();
+ panel_15.add(horizontalGlue_3);
+
+ Component verticalStrut_10 = Box.createVerticalStrut(5);
+ panel_14.add(verticalStrut_10);
+
+ _complexModeComponent = new ComplexModeComponent();
+ _complexModeComponent.setToolTipText("Describe how complex-valued Matlab arrays should be imported: only the real part, only the imaginary part, or both. In the latter, the real data will be saved in even channels, and imaginary data in odd channels.");
+ panel_14.add(_complexModeComponent);
+
+ }
+
+}
diff --git a/src/main/java/plugins/ylemontag/matlabimporter/MatlabImporterPlugin.java b/src/main/java/plugins/ylemontag/matlabimporter/MatlabImporterPlugin.java
new file mode 100644
index 0000000..0aa4500
--- /dev/null
+++ b/src/main/java/plugins/ylemontag/matlabimporter/MatlabImporterPlugin.java
@@ -0,0 +1,332 @@
+package plugins.ylemontag.matlabimporter;
+
+import icy.gui.dialog.MessageDialog;
+import icy.gui.frame.IcyFrame;
+import icy.gui.frame.progress.ProgressFrame;
+import icy.plugin.abstract_.PluginActionable;
+import icy.preferences.XMLPreferences;
+import icy.sequence.Sequence;
+import icy.system.thread.ThreadUtil;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Set;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+
+import plugins.ylemontag.matlabio.ComplexMode;
+import plugins.ylemontag.matlabio.DimensionMapping;
+import plugins.ylemontag.matlabio.MatlabImporter;
+import plugins.ylemontag.matlabio.gui.ComplexModeComponent;
+import plugins.ylemontag.matlabio.gui.DimensionMappingComponent;
+import plugins.ylemontag.matlabio.gui.DimensionMappingComponent.DimensionMappingChangedListener;
+import plugins.ylemontag.matlabio.gui.FileChooserComponent;
+import plugins.ylemontag.matlabio.gui.FileChooserComponent.FileChangedListener;
+import plugins.ylemontag.matlabio.gui.MatlabProgressFrame;
+import plugins.ylemontag.matlabio.lib.Controller;
+import plugins.ylemontag.matlabio.lib.MLMeta;
+
+/**
+ *
+ * @author Yoann Le Montagner
+ *
+ * Plugin to import .mat file as sequences
+ */
+public class MatlabImporterPlugin extends PluginActionable
+{
+ private FileChooserComponent _fileChooserComponent;
+ private DimensionMappingComponent _dimensionMappingComponent;
+ private ComplexModeComponent _complexModeComponent;
+ private JCheckBox _doPrefixComponent;
+ private VariableListComponent _variableListComponent;
+ private JButton _refreshButton;
+ private JButton _actionButton;
+ private File _file;
+ private MatlabImporter _importer;
+
+ @Override
+ public void run()
+ {
+ // GUI
+ IcyFrame frame = new IcyFrame("Matlab importer", true, true, true, true);
+ frame.setSize (500, 400);
+ frame.setSizeExternal(500, 400);
+ MainPanel mainPanel = new MainPanel();
+ frame.add(mainPanel);
+ addIcyFrame(frame);
+ frame.center();
+ frame.setVisible(true);
+ frame.requestFocus();
+ _fileChooserComponent = mainPanel.getFileComponent();
+ _dimensionMappingComponent = mainPanel.getDimensionMappingComponent();
+ _complexModeComponent = mainPanel.getComplexModeComponent();
+ _doPrefixComponent = mainPanel.getDoPrefixComponent();
+ _variableListComponent = mainPanel.getVariableComponent();
+ _refreshButton = mainPanel.getRefreshButton();
+ _actionButton = mainPanel.getActionButton();
+ retrievePersistentPrefix();
+ retrievePersistentDimensionMapping();
+ retrievePersistentComplexMode();
+ retrievePersistentDirectory();
+
+ // Listeners
+ _fileChooserComponent.addFileChangedListener(new FileChangedListener()
+ {
+ @Override
+ public void actionPerformed(File newFile) {
+ refreshVariableList(true, null);
+ updatePersistentDirectory();
+ }
+ });
+ _dimensionMappingComponent.addDimensionMappingChangedListener(new DimensionMappingChangedListener()
+ {
+ @Override
+ public void actionPerformed() {
+ updatePersistentDimensionMapping();
+ }
+ });
+ _complexModeComponent.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ updatePersistentComplexMode();
+ }
+ });
+ _doPrefixComponent.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ updatePersistentPrefix();
+ }
+ });
+ _refreshButton.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ refreshVariableList(false, _variableListComponent.getSelectedVariables());
+ }
+ });
+ _actionButton.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ executeImport();
+ }
+ });
+ _variableListComponent.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e) {
+ if(e.getButton()==1 && e.getClickCount()==2) {
+ executeImport();
+ }
+ }
+ });
+ }
+
+ /**
+ * Refresh the component that display the list of importable variables in
+ * the currently selected .mat file
+ */
+ private void refreshVariableList(boolean refreshFile, List<String> selectedVariables)
+ {
+ // Refresh the file from the dedicated component
+ if(refreshFile) {
+ _file = _fileChooserComponent.getSelectedFile();
+ }
+
+ // If no file is selected
+ _variableListComponent.clearRows();
+ _importer = null;
+ if(_file==null) {
+ return;
+ }
+
+ // Try to rebuild the importer
+ try {
+ _importer = new MatlabImporter(_file);
+ }
+ catch(IOException err) {
+ String message = "Cannot read the Matlab file " + _file.getPath();
+ MessageDialog.showDialog("Error", message, MessageDialog.ERROR_MESSAGE);
+ return;
+ }
+
+ // Refresh the list
+ Set<String> names = _importer.getImportableSequences();
+ for(String name : names) {
+ MLMeta meta = _importer.getMeta(name);
+ _variableListComponent.addRow(meta);
+ }
+
+ // Enforce the selection
+ if(selectedVariables!=null) {
+ _variableListComponent.setSelectedVariables(selectedVariables);
+ }
+ }
+
+ /**
+ * Retrieve the current prefix
+ */
+ private String getCurrentPrefix()
+ {
+ String retVal = "";
+ if(_doPrefixComponent.isSelected() && _file!=null) {
+ retVal = _file.getName();
+ int dotPosition = retVal.lastIndexOf('.');
+ if(dotPosition>=0) {
+ retVal = retVal.substring(0, dotPosition);
+ }
+ retVal += "/";
+ }
+ return retVal;
+ }
+
+ /**
+ * Do the importing job
+ */
+ private void executeImport()
+ {
+ final List<String> names = _variableListComponent.getSelectedVariables();
+ _variableListComponent.clearSelection();
+ for(final String name : names) {
+ final DimensionMapping mapping = _dimensionMappingComponent.getDimensionMapping();
+ final ComplexMode complexMode = _complexModeComponent.getComplexMode();
+ final String prefix = getCurrentPrefix();
+ final Controller controller = new Controller();
+ final ProgressFrame progressFrame = new MatlabProgressFrame("Importing sequence " + name, controller);
+ ThreadUtil.bgRun(new Runnable()
+ {
+ @Override
+ public void run() {
+ try {
+ Sequence seq = _importer.getSequence(name, mapping, complexMode, prefix+name, controller);
+ addSequence(seq);
+ }
+ catch(final IOException err) {
+ ThreadUtil.invokeLater(new Runnable()
+ {
+ @Override
+ public void run() {
+ System.err.println(err);
+ String message = "Cannot import the variable '" + name + "'";
+ MessageDialog.showDialog("Error", message, MessageDialog.ERROR_MESSAGE);
+ }
+ });
+ }
+ catch(Controller.CanceledByUser err) {}
+ finally {
+ ThreadUtil.invokeLater(new Runnable()
+ {
+ @Override
+ public void run() {
+ progressFrame.close();
+ }
+ });
+ }
+ }
+ });
+ }
+ }
+
+ /**
+ * Retrieve the persistent dimension mapping parameters
+ */
+ private void retrievePersistentDimensionMapping()
+ {
+ XMLPreferences prefs = getPreferences("DimensionMapping");
+ DimensionMapping mapping = _dimensionMappingComponent.getDimensionMapping();
+ int dimX = mapping.getDimensionX();
+ int dimY = mapping.getDimensionY();
+ int dimZ = mapping.getDimensionZ();
+ int dimT = mapping.getDimensionT();
+ int dimC = mapping.getDimensionC();
+ dimX = prefs.getInt("DimX", dimX);
+ dimY = prefs.getInt("DimY", dimY);
+ dimZ = prefs.getInt("DimZ", dimZ);
+ dimT = prefs.getInt("DimT", dimT);
+ dimC = prefs.getInt("DimC", dimC);
+ _dimensionMappingComponent.setDimensions(dimX, dimY, dimZ, dimT, dimC);
+ }
+
+ /**
+ * Update the persistent dimension mapping parameters
+ */
+ private void updatePersistentDimensionMapping()
+ {
+ XMLPreferences prefs = getPreferences("DimensionMapping");
+ DimensionMapping mapping = _dimensionMappingComponent.getDimensionMapping();
+ prefs.putInt("DimX", mapping.getDimensionX());
+ prefs.putInt("DimY", mapping.getDimensionY());
+ prefs.putInt("DimZ", mapping.getDimensionZ());
+ prefs.putInt("DimT", mapping.getDimensionT());
+ prefs.putInt("DimC", mapping.getDimensionC());
+ }
+
+ /**
+ * Retrieve the persistent directory
+ */
+ private void retrievePersistentDirectory()
+ {
+ XMLPreferences prefs = getPreferences("Directory");
+ String directoryPath = _fileChooserComponent.getCurrentDirectory().getAbsolutePath();
+ directoryPath = prefs.get("Path", directoryPath);
+ _fileChooserComponent.setCurrentDirectory(new File(directoryPath));
+ }
+
+ /**
+ * Update the persistent directory
+ */
+ private void updatePersistentDirectory()
+ {
+ XMLPreferences prefs = getPreferences("Directory");
+ prefs.put("Path", _fileChooserComponent.getCurrentDirectory().getAbsolutePath());
+ }
+
+ /**
+ * Retrieve the persistent complex mode parameter
+ */
+ private void retrievePersistentComplexMode()
+ {
+ XMLPreferences prefs = getPreferences("ComplexMode");
+ ComplexMode complexMode = _complexModeComponent.getComplexMode();
+ complexMode = ComplexMode.fromDescription(prefs.get("Name", complexMode.getDescription()));
+ if(complexMode!=null) {
+ _complexModeComponent.setComplexMode(complexMode);
+ }
+ }
+
+ /**
+ * Update the persistent complex mode
+ */
+ private void updatePersistentComplexMode()
+ {
+ XMLPreferences prefs = getPreferences("ComplexMode");
+ prefs.put("Name", _complexModeComponent.getComplexMode().getDescription());
+ }
+
+ /**
+ * Retrieve the persistent prefix parameter
+ */
+ private void retrievePersistentPrefix()
+ {
+ XMLPreferences prefs = getPreferences("Prefix");
+ boolean doPrefix = prefs.getBoolean("UseFilename", _doPrefixComponent.isSelected());
+ _doPrefixComponent.setSelected(doPrefix);
+ }
+
+ /**
+ * Update the persistent prefix parameter
+ */
+ private void updatePersistentPrefix()
+ {
+ XMLPreferences prefs = getPreferences("Prefix");
+ prefs.putBoolean("UseFilename", _doPrefixComponent.isSelected());
+ }
+}
diff --git a/src/main/java/plugins/ylemontag/matlabimporter/VariableListComponent.java b/src/main/java/plugins/ylemontag/matlabimporter/VariableListComponent.java
new file mode 100644
index 0000000..e5aedea
--- /dev/null
+++ b/src/main/java/plugins/ylemontag/matlabimporter/VariableListComponent.java
@@ -0,0 +1,129 @@
+package plugins.ylemontag.matlabimporter;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import javax.swing.JTable;
+import javax.swing.table.DefaultTableModel;
+import javax.swing.table.TableModel;
+import javax.swing.table.TableRowSorter;
+
+import plugins.ylemontag.matlabio.lib.MLMeta;
+
+/**
+ *
+ * @author Yoann Le Montagner
+ *
+ * Component used to display a list of Matlab objects contained in a .mat file
+ */
+public class VariableListComponent extends JTable
+{
+ private static final long serialVersionUID = 1L;
+
+ private DefaultTableModel _model;
+
+ /**
+ * Constructor
+ */
+ public VariableListComponent()
+ {
+ super();
+ _model = new Model();
+ setModel(_model);
+ TableRowSorter<TableModel> sorter = new TableRowSorter<TableModel>(_model);
+ setRowSorter(sorter);
+ }
+
+ /**
+ * Return the variable name corresponding to a given row. The row index is
+ * relative to the JTable (not to the model)
+ */
+ public String getVariableAt(int rowIndex)
+ {
+ return (String)getValueAt(rowIndex, 0);
+ }
+
+ /**
+ * Return the list of selected variables
+ */
+ public List<String> getSelectedVariables()
+ {
+ int[] selectedRows = getSelectedRows();
+ List<String> retVal = new LinkedList<String>();
+ for(int selectedRow : selectedRows) {
+ retVal.add(getVariableAt(selectedRow));
+ }
+ return retVal;
+ }
+
+ /**
+ * Set the list of selected variables
+ */
+ public void setSelectedVariables(List<String> selectedVariables)
+ {
+ clearSelection();
+ for(int r=0; r<getRowCount(); ++r) {
+ if(selectedVariables.contains(getVariableAt(r))) {
+ getSelectionModel().addSelectionInterval(r, r);
+ }
+ }
+ }
+
+ /**
+ * Add a row the table
+ */
+ public void addRow(MLMeta meta)
+ {
+ String name = meta.getName();
+ String dims = meta.getDimensionsAsString();
+ Boolean cplx = meta.getIsComplex();
+ String type = meta.getType().toString();
+ _model.addRow(new Object[] {name, type, cplx, dims});
+ }
+
+ /**
+ * Remove all the rows
+ */
+ public void clearRows()
+ {
+ _model.setRowCount(0);
+ }
+
+ /**
+ * Model used in the component
+ */
+ private static class Model extends DefaultTableModel
+ {
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructor
+ */
+ public Model()
+ {
+ super();
+ addColumn("Variable" );
+ addColumn("Type" );
+ addColumn("Complex" );
+ addColumn("Dimensions");
+ }
+
+ @Override
+ public boolean isCellEditable(int row, int column)
+ {
+ return false;
+ }
+
+ @Override
+ public int getColumnCount()
+ {
+ return 4;
+ }
+
+ @Override
+ public Class<?> getColumnClass(int columnIndex)
+ {
+ return columnIndex==2 ? Boolean.class : String.class;
+ }
+ }
+}
diff --git a/src/main/resources/icon-Matlab-function-caller.png b/src/main/resources/icon-Matlab-function-caller.png
new file mode 100644
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--
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