CHG: adapted .ijm examples (thanks to pyramids)

Author: xulman

src/main/ijm/DataStore-To-TIFFs.ijm

@@ -32,7 +32,7 @@ for (t = downloadTimePoint_FROM; t <= downloadTimePoint_TILL; t++) {
 	filename = outputDir+"/"+fileNameBeforeTPNumber+padding(t,zeroPaddingWidth)+fileNameAfterTPNumber;
 	print("Doing TP "+t+", that is a file: "+filename);
 
-	run("Read full image", "url="+host_port+" datasetid="+dataset+" timepoint="+t+" channel="+downloadFromThisChannel+" angle="+downloadThisAngle+" resolutionlevelsasstr=[[1, 1, 1]] versionasstr="+version+" timeout="+(timeout*1000)+" verboselog="+verboseDownload);
+	run("Read full image", "url="+host_port+" datasetid="+dataset+" versionasstr="+version+" timepoint="+t+" channel="+downloadFromThisChannel+" angle="+downloadThisAngle+" resolutionlevelsasstr=[[1, 1, 1]] timeout="+(timeout*1000)+" verboselog="+verboseDownload);
 
 	saveAs("Tiff", filename);
 	close();

src/main/ijm/TIFFs_Downscale_And_To_DataStore.ijm renamed to src/main/ijm/TIFFs-Downscale-And-To-DataStore.ijm

@@ -0,0 +1,65 @@
+#@ String(persistkey="datasetserverurl") host_port
+#@ String(persistkey="datasetdatasetid") dataset
+#@ String(description="Use single number like 0,1,2 or keywords latest or new") version = "latest"
+
+#@ int(min="0") uploadIntoThisChannel
+#@ int(min="0") uploadIntoThisAngle
+#@ int(min="0") uploadTimePoint_FROM
+#@ int(min="0") uploadTimePoint_TILL
+
+#@ String(description="The part of file name before the time-point running numbers", default="img") fileNameBeforeTPNumber
+#@ int(description="Pad running numbers with zeros up to the given width, set to 0 for no padding.", min="0", default="0") zeroPaddingWidth
+#@ String(description="The part of file name right after the time-point running numbers", default=".tif") fileNameAfterTPNumber = ".tif"
+#@ File(style="directory", description="Folder with the above defined files") inputDir
+
+#@ boolean verboseUpload = false
+#@ int(min="0", label="Timeout in seconds, e.g. 60") timeout
+
+//fixup boolean: 1 -> true
+if (verboseUpload == 1) { verboseUpload = "true"; }
+
+function padding(number, width) {
+	if (width > 0) {
+		numStr = "00000000000000000000"+number;
+		return substring(numStr, numStr.length-width);
+	} else {
+		return number;
+	}
+}
+
+function justSaveAsLevel(resLevelX,resLevelY,resLevelZ) {
+	run("Write full image", "url="+host_port+" datasetid="+dataset+" versionasstr="+version+" timepoint="+t+" channel="+uploadIntoThisChannel+" angle="+uploadIntoThisAngle+" resolutionlevelsasstr=[["+resLevelX+", "+resLevelY+", "+resLevelZ+"]] timeout="+(timeout*1000)+" verboselog="+verboseUpload+" uploadrespyramids=true");
+}
+
+function scaleAndSave(refMainImg, resLevelX,resLevelY,resLevelZ) {
+	xFac = 1/resLevelX;
+	yFac = 1/resLevelY;
+	zFac = 1/resLevelZ;
+	selectImage(refMainImg);
+	run("Scale...", "x="+xFac+" y="+yFac+" z="+zFac+" interpolation=None process create");
+	justSaveAsLevel(resLevelX,resLevelY,resLevelZ);
+	close();
+	//NB: close() is counterpart to "create" in the run() above
+}
+
+print("Uploading started....");
+for (t = uploadTimePoint_FROM; t <= uploadTimePoint_TILL; t++) {
+	filename = inputDir+"/"+fileNameBeforeTPNumber+padding(t,zeroPaddingWidth)+fileNameAfterTPNumber;
+	print("Doing TP "+t+", that is a file: "+filename);
+
+	open(filename);
+	mainImgID = getImageID();
+
+	print("Saving resolution level 1");
+	justSaveAsLevel(1,1,1);
+
+	print("Saving resolution level 2");
+	scaleAndSave(mainImgID, 2,2,1);
+
+	print("Saving resolution level 3");
+	scaleAndSave(mainImgID, 4,4,1);
+
+	selectImage(mainImgID);
+	close();
+}
+print("Uploading finished....");