Adds MRI previewer for NIFTY (.nii) file format. (#241)

* Adds MRI previewer for NIFTY (.nii) file format.

* deleted vim swap files

* Added application/x-gzip to file types on which nii previewer runs on.

* Added changelog and contributors.

Co-authored-by: Luigi Marini <[email protected]>
Co-authored-by: Luigi Marini <[email protected]>

Author: pgroves

CHANGELOG.md

@@ -8,6 +8,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ## Unreleased
 
+### Added
+- MRI previewer for NIFTY (.nii) files.
+
 ### Fixed
 - Send email to all admins in a single email when a user submits 'Request access' for a space
 - Send email to all admins and request user in a single email when any admin accepts/rejects 'Request access' for a space [#330](https://github.com/clowder-framework/clowder/issues/330)

CONTRIBUTORS.md

@@ -31,6 +31,7 @@ Following is a list of contributors in alphabetical order:
 - Mike Lambert
 - Nicholas Tenczar
 - Nishant Nayudu
+- Peter Groves
 - Rob Kooper
 - Rui Liu
 - Sandeep Puthanveetil Satheesan

conf/mimetypes.conf

@@ -134,4 +134,5 @@ mimetype.nra=application/simsnra
 mimetype.spe=application/simsspe
 mimetype.Spe=application/simsspe
 mimetype.xrdml=application/xray-xrdml
-mimetype.xnra=application/simsxnra
+mimetype.xnra=application/simsxnra
+mimetype.nii=image/nii

public/javascripts/previewers/mri-papaya/README.md

@@ -0,0 +1,37 @@
+#MRI previewer based on the Papaya JS library
+
+## Papaya Library
+Papaya is a javascript component for viewing MRI images. This integration only
+currently supports NIFTI images (.nii and .nii.gz files).
+
+Homepage: https://rii-mango.github.io/Papaya/
+Live demo: https://papaya.greenant.net/
+Source: https://github.com/rii-mango/Papaya
+
+## Clowder Previewer
+
+![Clowder MRI Previewer Screenshot](clowder-mri-papaya-screenshot.png)
+
+TODO: Support for DICOM images is possible, but the integration is harder b/c
+a single DICOM volume is a directory full of image files which must be queried
+for through Clowder and then fed to the jquery component.
+
+## Build
+
+The assets in this previewer (clowder/public/javascripts/previewers/mri-papaya)
+can be replicated with the following procedure. The BUILD_SHA below is from May 5, 2019, which
+was the HEAD of the project's `master` branch as of April 15 2021. 
+
+Note that the `-nojquery` flag must be included or it will bundle a version of jquery that is
+incompatible with Clowder's.
+
+```
+BUILD_SHA=782a19341af77a510d674c777b6da46afb8c65f1
+git clone [email protected]:rii-mango/Papaya.git
+cd Papaya
+git checkout $BUILD_SHA
+./papaya-builder.sh -nojquery
+```
+
+The assets will then be in the `build/` directory
+

public/javascripts/previewers/mri-papaya/clowder-mri-papaya-screenshot.png

@@ -0,0 +1,30 @@
+(function ($, Configuration) {
+
+    var scriptElem = document.createElement("script");
+    scriptElem.type = "text/javascript";
+    scriptElem.src = Configuration.previewer + "/papaya.js";
+    $(Configuration.tab).append(scriptElem);
+
+    var styleSheetLink = document.createElement("link");
+    styleSheetLink.rel = 'stylesheet';
+    styleSheetLink.href = Configuration.previewer + "/papaya.css";
+    $(Configuration.tab).append(styleSheetLink);
+
+    var params = [];
+    var papayaDivId = "papayaMain";
+    params['images'] = [Configuration.url];
+
+    //force the bottom control bar always on or the buttons will pop up in a weird place in the page
+    params['showControlBar'] = true;
+
+    //If you don't want the bottom controls, do this instead of showControlBar
+    //params['showControls'] = false;
+
+    var papayaDiv = document.createElement("div")
+    papayaDiv.setAttribute("id", papayaDivId);
+    $(Configuration.tab).append(papayaDiv);
+    papaya.Container.addViewer(papayaDivId, params);
+
+}(jQuery, Configuration));
+
+

public/javascripts/previewers/mri-papaya/mri-papaya.js

@@ -0,0 +1,6 @@
+{
+	"name": "interactive_mri_viewer_for_nii_files",
+	"main": "mri-papaya.js",
+	"file": true,
+	"contentType": ["image/nii", "application/x-gzip"]
+}