# Name: plugins_TP

# Description:
# Somewhat idiosyncratic collection for Nuclear Medicine

# Author: J. Anthony Parker, MD PhD
# Version: 0.0
# Date: 2008/05/19
# Requires: not known; Works with ImageJ 1.39t

# Extract jar contents and generate tp_collection.jar file using:
#     cd /Applications/ImageJ/tp_collection/extractedJar
#     jar xf ../../plugins/jars/Animated_Gif.jar
#     jar xf ../../plugins/jars/Excel_Writer.jar
#     jar xf ../../plugins/jars/nifti_io.jar
#     jar xf ../../plugins/jars/QuickTime_Opener.jar
#     jar xf ../../plugins/jars/QuickTime_Plugins.jar
#     cd /Applications/ImageJ/tp_collection
#     jar cf tp_collection.jar plugins.config
#     jar uf tp_collection.jar -C ../plugins/Align\ Stacks .
#     jar uf tp_collection.jar -C ../plugins/Input-Output .
#     jar uf tp_collection.jar -C ../plugins/NucMed .
#     jar uf tp_collection.jar -C ../plugins/Stacks .
#     jar uf tp_collection.jar -C extractedJar .
#     jar i tp_collection.jar

Plugins>Align Stacks, "Align3 TP", Align3_TP
Plugins>Align Stacks, "Display3 TP", Display3_TP
Plugins>Align Stacks, "Fusion TP", Fusion_TP
Plugins>Align Stacks, "Reorient3 TP", Reorient3_TP
Plugins>Align Stacks, "Show AlignmentTP", Show_AlignmentTP
Plugins>Align Stacks, "Test Optimize", Test_Optimize
Plugins>Align Stacks, "To AxialTP", To_AxialTP
Plugins>Align Stacks, "To CoronalTP", To_CoronalTP
Plugins>Align Stacks, "To SagitalTP", To_SagitalTP
Plugins>Align Stacks, "TwoD HistogramTP", TwoD_HistogramTP
Plugins>Input-Output, "DICOM sort", DICOM_sort
Plugins>Input-Output, "Dicom Rewriter", dicom_rewriter
Plugins>Input-Output, "Excel Toolbar ...", Excel_Toolbar
Plugins>Input-Output, "Jimi Reader", Jimi_Reader
Plugins>Input-Output, "Jimi Writer", Jimi_Writer
Plugins>Input-Output, "PDF Writer", PDF_Writer
Plugins>NucMed, "AtoN TP", AtoN_TP
Plugins>NucMed, "Compartments TP", Compartments_TP
Plugins>NucMed, "ConvertLUT TP", ConvertLUT_TP
Plugins>NucMed, "Crop Update OriginTP", Crop_Update_OriginTP
Plugins>NucMed, "DICOM RescaleTP", DICOM_RescaleTP
Plugins>NucMed, "Dispose All Windows", Dispose_All_Windows
Plugins>NucMed, "Fit LineTP", Fit_LineTP
Plugins>NucMed, "LUT Values TP", LUT_Values_TP
Plugins>NucMed, "Lookup Tables", Lookup_Tables
Plugins>NucMed, "NucMed Open", NucMed_Open
Plugins>NucMed, "Project TP", Project_TP
Plugins>NucMed, "Reorder Gated Slices", Reorder_Gated_Slices
Plugins>NucMed, "Save As Interfile", Save_As_Interfile
Plugins>Stacks, "Concatenator", Concatenator_
Plugins>Stacks, "Stack Builder", Stack_Builder
Plugins>Stacks, "Stack Normalizer", Stack_Normalizer
Plugins>Stacks, "Stack Splitter", Stack_Splitter
#Plugins>Stacks, "Volume Viewer", Volume_Viewer
Help>About Plugins, "About Align3 TP", Align3_TP("about")
Help>About Plugins, "About Display3 TP", Display3_TP("about")
Help>About Plugins, "About Fusion TP", Fusion_TP("about")
Help>About Plugins, "About Reorient3 TP", Reorient3_TP("about")
Help>About Plugins, "About To AxialTP", To_AxialTP("about")
Help>About Plugins, "About To CoronalTP", To_CoronalTP("about")
Help>About Plugins, "About To SagitalTP", To_SagitalTP("about")
Help>About Plugins, "About TwoD HistogramTP", TwoD_HistogramTP("about")
Help>About Plugins, "About AtoN TP", AtoN_TP("about")
Help>About Plugins, "About Compartments TP", Compartments_TP("about")
Help>About Plugins, "About Crop Update OriginTP", Crop_Update_OriginTP("about")
Help>About Plugins, "About DICOM RescaleTP", DICOM_RescaleTP("about")
Help>About Plugins, "About NucMed Open", NucMed_Open("about")
Help>About Plugins, "About Save As Interfile", Save_As_Interfile("about")

# Installs the Excel_Writer plugins in the File>Save As menu
File>Save As, "Excel...", Excel_Writer
File>Save As, "XY Coordinates to Excel...", Save_XY_Coordinates_to_Excel
# Installs the Excel_Writer_GUI plugin in the Plugin menu
Plugins, "Excel ToolBar...", Excel_Writer_GUI

# Name: nifti_io
# Author: Guy Williams
# Version: 1.04
# Date: 2007/6/29 
# Requires: ImageJ 1.42h
# Generate jar file using: jar cvfM NIfTI_IO.jar *


File>Import, "NIfTI-Analyze", Nifti_Reader("")
File>Save As, "Analyze (NIfTI-1)", Nifti_Writer("::NIFTI_ANALYZE:")
File>Save As, "NIfTI-1", Nifti_Writer("::NIFTI_FILE:")
File>Save As, "Analyze 7.5", Nifti_Writer("::ANALYZE_7_5:")
Analyze>Tools, "Coordinate Viewer", Coordinate_Viewer("")

# Name: QuickTime_Movie_Opener

# Description:
# This plugin opens a QuickTime move as a stack

# Authors: Wayne Rasband and Jeff Hardin
# Date: 2004/12/13
# Requires: QuickTime for Java

# Generate the jar file using: "jar cvfM QuickTime_Opener.jar *"

File>Import, "QuickTime...", QT_Movie_Opener
# Name: QuickTime_Plugins

# Description:
# These plugin opens a QuickTime movies as a stack, save
# a stack as a QuickTime move, play a QuickTime movie
# and capture video using QuickTime.

# Authors: Wayne Rasband and Jeff Hardin
# Date: 2005/10/11
# Requires: QuickTime for Java

# Generate the jar file using: "jar cvfM QuickTime_Plugins.jar *"

File>Import, "Using QuickTime...", QT_Movie_Opener
File>Import, "Video", QuickTime_Capture
File>Import, "QuickTime Player...", QT_Movie_Player
File>Save As, "QuickTime Movie...", QuickTime_Writer