initial commit

NIFTI-Imaging · Mar 14, 2019 · 3ed6588 · 3ed6588
commit 3ed6588
Show file tree

Hide file tree

Showing 19 changed files with 2,145 additions and 0 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,32 @@
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
diff --git a/README.md b/README.md
@@ -0,0 +1,15 @@
+# VERSIONS
+## v1.0.0 data intended for testing `gifti_clib` version 1.0.0
+
+# gifti-test-data
+
+A repository for storing test data used for the gifti project.  This repository is used as a storage location for the `gifti_clib` project initial conversion to github, and may be replaced with a more sustainable/modular solution in the future.
+
+Releases of this data set will provide a link to a tarball that
+can be used inside of the `gifti_clib` project for testing
+the functionality of those programs.
+
+
+## Data copied from [caret gifti files](https://www.nitrc.org/frs/download.php/1894/caret_gifti_files.zip)
+
+The Caret data is a convenience copy in the local caret_data diredtory.
diff --git a/caret_data/Human.colin.R.FUNCTIONAL.71723.func.gii b/caret_data/Human.colin.R.FUNCTIONAL.71723.func.gii
diff --git a/gifti_regress_data/LT.Index.gii b/gifti_regress_data/LT.Index.gii
@@ -0,0 +1,137 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE GIFTI SYSTEM "http://gifti.projects.nitrc.org/gifti.dtd">
+<GIFTI Version="1.0"  NumberOfDataArrays="3">
+   <!-- from color.table.gii, but without the bad element or attribute -->
+   <MetaData>
+      <MD>
+         <Name><![CDATA[Caret-Version]]></Name>
+         <Value><![CDATA[5.511]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[date]]></Name>
+         <Value><![CDATA[Wed Nov 21 14:53:44 2007]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[encoding]]></Name>
+         <Value><![CDATA[XML]]></Value>
+      </MD>
+   </MetaData>
+   <LabelTable>
+      <Label Index="17" Red="0.62" Green="0.62" Blue="0.62" Alpha="1">PickleCenter</Label>
+      <Label Index="23" Red="0.5" Green="0.5" Blue="0.5" Alpha="1">DonutRegion</Label>
+      <Label Index="29" Red="1" Green="0" Blue="0" Alpha="1"><![CDATA[MyCDATARegion]]></Label>
+   </LabelTable>
+   <DataArray Intent="NIFTI_INTENT_POINTSET"
+              DataType="NIFTI_TYPE_FLOAT32"
+              ArrayIndexingOrder="RowMajorOrder"
+              Dimensionality="2"
+              Dim0="10"
+              Dim1="3"
+              Encoding="ASCII"
+              Endian="LittleEndian"
+              ExternalFileName=""
+              ExternalFileOffset="">
+      <MetaData>
+         <MD>
+            <Name><![CDATA[AnatomicalStructurePrimary]]></Name>
+            <Value><![CDATA[CortexLeft]]></Value>
+         </MD>
+         <MD>
+            <Name><![CDATA[AnatomicalStructureSecondary]]></Name>
+            <Value><![CDATA[Pial]]></Value>
+         </MD>
+         <MD>
+            <Name><![CDATA[GeometricType]]></Name>
+            <Value><![CDATA[Anatomical]]></Value>
+         </MD>
+         <MD>
+            <Name><![CDATA[UniqueID]]></Name>
+            <Value><![CDATA[{e31cd8a6-bba6-4a1f-a26b-eb7337909a1c}]]></Value>
+         </MD>
+      </MetaData>
+      <CoordinateSystemTransformMatrix>
+         <DataSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></DataSpace>
+         <TransformedSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></TransformedSpace>
+         <MatrixData>
+            1.000000 0.000000 0.000000 0.000000 
+            0.000000 1.000000 0.000000 0.000000 
+            0.000000 0.000000 1.000000 0.000000 
+            0.000000 0.000000 0.000000 1.000000 
+         </MatrixData>
+      </CoordinateSystemTransformMatrix>
+      <Data>
+         -16.072010 -66.187515 21.266994 
+         -16.705893 -66.054337 21.232786 
+         -17.614349 -65.401642 21.071466 
+         -16.227057 -66.076813 20.798044 
+         -17.294590 -65.592651 20.492159 
+         -3.359210 106.892578 42.960064 
+         -1.987704 107.147110 44.961926 
+         0.831468 107.310471 42.439121 
+         -2.223662 107.080841 44.305389 
+         -2.483269 107.022430 44.894073 
+      </Data>
+   </DataArray>
+   <DataArray Intent="NIFTI_INTENT_VECTOR"
+              DataType="NIFTI_TYPE_FLOAT32"
+              ArrayIndexingOrder="RowMajorOrder"
+              Dimensionality="2"
+              Dim0="10"
+              Dim1="3"
+              Encoding="ASCII"
+              Endian="LittleEndian"
+              ExternalFileName=""
+              ExternalFileOffset="">
+      <MetaData>
+         <MD>
+            <Name><![CDATA[UniqueID]]></Name>
+            <Value><![CDATA[{ae03859c-3bd6-409e-9d95-b693380d0bdf}]]></Value>
+         </MD>
+      </MetaData>
+      <Data>
+         -0.222756 -0.939575 -0.259960 
+         -0.379413 -0.911859 -0.156711 
+         -0.478813 -0.874120 -0.081563 
+         -0.191100 -0.919591 -0.343267 
+         -0.417368 -0.905682 -0.074461 
+         -0.347235 0.937524 -0.021808 
+         -0.289554 0.957094 -0.011422 
+         0.038875 0.992079 -0.119447 
+         -0.268772 0.963188 -0.005467 
+         -0.288021 0.956546 0.045433 
+      </Data>
+   </DataArray>
+   <DataArray Intent="NIFTI_INTENT_TRIANGLE"
+              DataType="NIFTI_TYPE_INT32"
+              ArrayIndexingOrder="RowMajorOrder"
+              Dimensionality="2"
+              Dim0="10"
+              Dim1="3"
+              Encoding="ASCII"
+              Endian="LittleEndian"
+              ExternalFileName=""
+              ExternalFileOffset="">
+      <MetaData>
+         <MD>
+            <Name><![CDATA[TopologicalType]]></Name>
+            <Value><![CDATA[CLOSED]]></Value>
+         </MD>
+         <MD>
+            <Name><![CDATA[UniqueID]]></Name>
+            <Value><![CDATA[{52f9c071-75ea-4e42-bde9-3d9ba3930b94}]]></Value>
+         </MD>
+      </MetaData>
+      <Data>
+         0 1 3 
+         4 3 1 
+         0 30 1 
+         31 1 30 
+         0 3 34 
+         141184 141431 141604 
+         141588 141700 141589 
+         141427 141433 141434 
+         141706 141710 141707 
+         141416 141185 141178 
+      </Data>
+   </DataArray>
+</GIFTI>
diff --git a/gifti_regress_data/ascii.misc.gii b/gifti_regress_data/ascii.misc.gii
@@ -0,0 +1,152 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE GIFTI SYSTEM "http://gifti.projects.nitrc.org/gifti.dtd">
+<GIFTI Version="1.0"  NumberOfDataArrays="3" OtherGiftiAttrib="useless.attrib">
+   <MetaData>
+      <MD>
+         <Name><![CDATA[Caret-Version]]></Name>
+         <Value><![CDATA[5.511]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[date]]></Name>
+         <Value><![CDATA[Wed Nov 21 14:53:44 2007]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[encoding]]></Name>
+         <Value><![CDATA[XML]]></Value>
+      </MD>
+   </MetaData>
+   <BadEle>This is a bad element.
+      Competition is bad.
+      Oxygen is good.
+      I like Jello.
+      <SonofBad>
+         Evil is born.
+      </SonofBad>
+   </BadEle>
+   <LabelTable>
+      <Label Key="17" Red="0.37" Green="0.39" Blue="0.41" Alpha="0.43">PickleCenter</Label>
+      <Label Key="23" Red="0.57" Green="0.59" Blue="0.61" Alpha="0.63">DonutRegion</Label>
+      <Label Key="29" Red="0.77" Green="0.79" Blue="0.81" Alpha="0.83"><![CDATA[MyCDATARegion]]></Label>
+   </LabelTable>
+   <!-- my comment: this has nothing to do with potato chips-->
+   <!-- note: changed nnodes from 143479 to 10 -->
+   <DataArray Intent="NIFTI_INTENT_POINTSET"
+              DataType="NIFTI_TYPE_FLOAT32"
+              ArrayIndexingOrder="RowMajorOrder"
+              Dimensionality="2"
+              Dim0="10"
+              Dim1="3"
+              Encoding="ASCII"
+              Endian="LittleEndian"
+              ExtraDAAtr="XtraDAattribute"
+              ExternalFileName=""
+              ExternalFileOffset="">
+      <MetaData>
+         <MD>
+            <Name><![CDATA[AnatomicalStructurePrimary]]></Name>
+            <Value><![CDATA[CortexLeft]]></Value>
+         </MD>
+         <MD>
+            <Name>name: the MD pickles</Name>
+            <Value>value: are MD yummy</Value>
+         </MD>
+         <MD>
+            <Name><![CDATA[AnatomicalStructureSecondary]]></Name>
+            <Value><![CDATA[Pial]]></Value>
+         </MD>
+         <MD>
+            <Name><![CDATA[GeometricType]]></Name>
+            <Value><![CDATA[Anatomical]]></Value>
+         </MD>
+         <MD>
+            <Name><![CDATA[UniqueID]]></Name>
+            <Value><![CDATA[{e31cd8a6-bba6-4a1f-a26b-eb7337909a1c}]]></Value>
+         </MD>
+      </MetaData>
+      <CoordinateSystemTransformMatrix>
+         <DataSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></DataSpace>
+         <TransformedSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></TransformedSpace>
+         <MatrixData>
+            1.000000 0.000000 0.000000 0.000000 
+            0.000000 1.000000 0.000000 0.000000 
+            0.000000 0.000000 1.000000 0.000000 
+            0.000000 0.000000 0.000000 1.000000 
+         </MatrixData>
+      </CoordinateSystemTransformMatrix>
+      <Data>
+         -16.072010 -66.187515 21.266994 
+         -16.705893 -66.054337 21.232786 
+         -17.614349 -65.401642 21.071466 
+         -16.227057 -66.076813 20.798044 
+         -17.294590 -65.592651 20.492159 
+         -3.359210 106.892578 42.960064 
+         -1.987704 107.147110 44.961926 
+         0.831468 107.310471 42.439121 
+         -2.223662 107.080841 44.305389 
+         -2.483269 107.022430 44.894073 
+      </Data>
+   </DataArray>
+   <DataArray Intent="NIFTI_INTENT_VECTOR"
+              DataType="NIFTI_TYPE_FLOAT32"
+              ArrayIndexingOrder="RowMajorOrder"
+              Dimensionality="2"
+              Dim0="10"
+              Dim1="3"
+              Encoding="ASCII"
+              Endian="LittleEndian"
+              ExternalFileName=""
+              ExternalFileOffset="">
+      <MetaData>
+         <MD>
+            <Name><![CDATA[UniqueID]]></Name>
+            <Value><![CDATA[{ae03859c-3bd6-409e-9d95-b693380d0bdf}]]></Value>
+         </MD>
+      </MetaData>
+      <Data>
+         -0.222756 -0.939575 -0.259960 
+         -0.379413 -0.911859 -0.156711 
+         -0.478813 -0.874120 -0.081563 
+         -0.191100 -0.919591 -0.343267 
+         -0.417368 -0.905682 -0.074461 
+         -0.347235 0.937524 -0.021808 
+         -0.289554 0.957094 -0.011422 
+         0.038875 0.992079 -0.119447 
+         -0.268772 0.963188 -0.005467 
+         -0.288021 0.956546 0.045433 
+      </Data>
+   </DataArray>
+   <!-- note: changed nnodes from 286954 to 10 -->
+   <DataArray Intent="NIFTI_INTENT_TRIANGLE"
+              DataType="NIFTI_TYPE_INT32"
+              ArrayIndexingOrder="RowMajorOrder"
+              Dimensionality="2"
+              Dim0="10"
+              Dim1="3"
+              Encoding="ASCII"
+              Endian="LittleEndian"
+              ExternalFileName=""
+              ExternalFileOffset="">
+      <MetaData>
+         <MD>
+            <Name><![CDATA[TopologicalType]]></Name>
+            <Value><![CDATA[CLOSED]]></Value>
+         </MD>
+         <MD>
+            <Name><![CDATA[UniqueID]]></Name>
+            <Value><![CDATA[{52f9c071-75ea-4e42-bde9-3d9ba3930b94}]]></Value>
+         </MD>
+      </MetaData>
+      <Data>
+         0 1 3 
+         4 3 1 
+         0 30 1 
+         31 1 30 
+         0 3 34 
+         141184 141431 141604 
+         141588 141700 141589 
+         141427 141433 141434 
+         141706 141710 141707 
+         141416 141185 141178 
+      </Data>
+   </DataArray>
+</GIFTI>