Added support for TIFF files

Biofrontiers-ALMC · Apr 13, 2020 · 7e5e841 · 7e5e841
1 parent e1191c9
commit 7e5e841
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Showing 2 changed files with 35 additions and 17 deletions.
diff --git a/build/Bioformats Image Toolbox.prj b/build/Bioformats Image Toolbox.prj
@@ -1,14 +1,14 @@
 <deployment-project plugin="plugin.toolbox" plugin-version="1.0">
-  <configuration build-checksum="1629181179" file="D:\Jian\Documents\Projects\coreCode\bioformats-image\code\build\Bioformats Image Toolbox.prj" location="D:\Jian\Documents\Projects\coreCode\bioformats-image\code\build" name="Bioformats Image Toolbox" target="target.toolbox" target-name="Package Toolbox">
-    <param.appname>Bioformats Image Toolbox (v1.1.0)</param.appname>
+  <configuration build-checksum="1629181179" file="D:\Projects\Bioformats Image Toolbox\code\build\Bioformats Image Toolbox.prj" location="D:\Projects\Bioformats Image Toolbox\code\build" name="Bioformats Image Toolbox" target="target.toolbox" target-name="Package Toolbox">
+    <param.appname>Bioformats Image Toolbox (v1.2.0)</param.appname>
     <param.authnamewatermark>Jian Wei Tay</param.authnamewatermark>
     <param.email>jian.tay@colorado.edu</param.email>
     <param.company>University of Colorado Boulder</param.company>
     <param.summary>MATLAB re-implementation of the Bioformats Image Toolbox by the OME group</param.summary>
     <param.description />
     <param.screenshot>${PROJECT_ROOT}\BioformatsImageIcon.png</param.screenshot>
-    <param.version>1.1.0</param.version>
-    <param.output>${PROJECT_ROOT}\Bioformats Image Toolbox (v1.1.0).mltbx</param.output>
+    <param.version>1.2.0</param.version>
+    <param.output>${PROJECT_ROOT}\Bioformats Image Toolbox (v1.2.0).mltbx</param.output>
     <param.products.name />
     <param.products.id />
     <param.products.version />
@@ -22,10 +22,7 @@
     <param.registered.apps />
     <param.docs />
     <param.getting.started.guide />
-    <param.matlabpath.excludes>
-      <item>/BioformatsImage/bfmatlab</item>
-      <item>/docs</item>
-    </param.matlabpath.excludes>
+    <param.matlabpath.excludes />
     <param.javaclasspath.excludes>
       <item>/BioformatsImage/bfmatlab/bioformats_package.jar</item>
     </param.javaclasspath.excludes>
@@ -64,6 +61,7 @@
       <param.registered.apps />
       <param.docs />
       <param.getting.started.guide />
+      <param.matlabpath.excludes />
       <param.exported.on.package />
       <param.required.addons />
       <param.matlab.project.id />
@@ -83,17 +81,16 @@
       <param.additional.sw.linux.url />
     </unset>
     <fileset.rootdir>
-      <file>D:\Jian\Documents\Projects\coreCode\bioformats-image\code\tbx</file>
+      <file>D:\Projects\Bioformats Image Toolbox\code\tbx</file>
     </fileset.rootdir>
     <fileset.rootfiles>
-      <file>D:\Jian\Documents\Projects\coreCode\bioformats-image\code\tbx\BioformatsImage</file>
-      <file>D:\Jian\Documents\Projects\coreCode\bioformats-image\code\tbx\docs</file>
+      <file>D:\Projects\Bioformats Image Toolbox\code\tbx\BioformatsImage</file>
     </fileset.rootfiles>
     <fileset.depfun.included />
     <fileset.depfun.excluded />
     <fileset.package />
     <build-deliverables>
-      <file location="${PROJECT_ROOT}" name="Bioformats Image Toolbox (v1.1.0).mltbx" optional="false">D:\Jian\Documents\Projects\coreCode\bioformats-image\code\build\Bioformats Image Toolbox (v1.1.0).mltbx</file>
+      <file location="${PROJECT_ROOT}" name="Bioformats Image Toolbox (v1.2.0).mltbx" optional="false">D:\Projects\Bioformats Image Toolbox\code\build\Bioformats Image Toolbox (v1.2.0).mltbx</file>
     </build-deliverables>
     <workflow />
     <matlab>

diff --git a/tbx/BioformatsImage/BioformatsImage.m b/tbx/BioformatsImage/BioformatsImage.m
@@ -272,8 +272,19 @@
         function chNames = get.channelNames(obj)
             chNames = cell(1,obj.sizeC);
 
-            for iC = 1:obj.sizeC
-                chNames{iC} = obj.metadata.getChannelName(0, iC - 1).char;
+            %Handle TIFF files
+            [~, ~, fExt] = fileparts(obj.filename);
+            switch lower(fExt)
+
+                case {'.tif', '.tiff'}
+                    for iC = 1:obj.sizeC
+                       chNames{iC} = int2str(iC); 
+                    end
+
+                otherwise
+                    for iC = 1:obj.sizeC
+                        chNames{iC} = obj.metadata.getChannelName(0, iC - 1).char;
+                    end
             end
         end
 
@@ -429,7 +440,7 @@ function delete(obj)
             end
 
         end
-
+                
         function [timestamps, tsunits] = getTimestamps(obj, iZ, iC, varargin)
             %GETTIMESTAMPS  Get timestamps from the specified channel
             %
@@ -447,6 +458,17 @@ function delete(obj)
             ip.addOptional('TimeRange',Inf,@(x) all(isinf(x)) || isnumeric(x));
             ip.parse(varargin{:});
 
+            %Handle TIFF files
+            [~, ~, fExt] = fileparts(obj.filename);
+            switch lower(fExt)
+
+                case {'.tif', '.tiff'}
+                    timestamps = NaN;
+                    tsunits = 'Not available';
+                    return
+
+            end
+
             %Resolve channel name
             iC = obj.channelname2ind(iC);
 
@@ -458,8 +480,7 @@ function delete(obj)
 
             %Initialize a vector for the timestamps
             timestamps = zeros(1, numel(timeRange));
-
-
+
                 for iT = timeRange
                     %Resolve the bioformats index
                     bfIndex = obj.getIndex(iZ,iC,iT);