commit 12f926de284cefeeb02f071be1ffe2f3530ff628
Author: Fischer Robert <robert.fischer@psi.ch>
Date:   Fri Oct 25 11:12:10 2024 +0200

    initial commit

diff --git a/Import_VOL_ImageJ.ijm b/Import_VOL_ImageJ.ijm
new file mode 100644
index 0000000..0493b72
--- /dev/null
+++ b/Import_VOL_ImageJ.ijm
@@ -0,0 +1,73 @@
+/* README: 
+ * This macro imports a VOL file into ImageJ using the information contained inside the corresponding PCR file. If no PCR is found,
+ * the user can input the information required to perform the action manually or provide the PCR file.
+ * 
+ * Execution:
+ * runMacro("...path.../Import_VOL.ijm");  	Opens a selected VOL file
+ * 
+ * Changelog:
+ * 2018.01.22 	Created		MR54
+ * 2021.03.12	Datos Ac update, Adapted Linenumbers to new header	CC54
+ * 
+ */
+ 
+// Select VOL file and extract PCR file name
+filePath = File.openDialog("Select VOL file to import");
+tempPath = split(filePath,".");
+pcrPath = tempPath[0]+".pcr";
+pcrSizeX = 0;
+pcrSizeY = 0;
+pcrSizeZ = 0;
+
+while (pcrSizeX == 0 || pcrSizeY == 0 || pcrSizeZ == 0) {
+	
+	if (File.exists(pcrPath)) {
+		
+		// Extract import parameters from pcr file
+		pcrContent = File.openAsString(pcrPath);
+		pcrLines = split(pcrContent,"\n");
+		for (i=0; i<pcrLines.length; i++) {
+			splitline = split(pcrLines[i],"=");
+			if (splitline[0] == "Volume_SizeX") {
+				pcrSizeX = splitline[1];
+			}
+			if (splitline[0] == "Volume_SizeY") {
+				pcrSizeY = splitline[1];
+			}
+			if (splitline[0] == "Volume_SizeZ") {
+				pcrSizeZ = splitline[1];
+			}
+		}
+		print(pcrSizeX);
+		print(pcrSizeY);
+		print(pcrSizeZ);
+		
+	} else {
+		
+		// No PCR file found
+		Dialog.create("Error");
+		Dialog.addMessage("There was no PCR file with the same name found.\nPlease enter the location of the PCR file or enter the dimensions manually.");
+		Dialog.addNumber("SizeX",0);
+		Dialog.addNumber("SizeY",0);
+		Dialog.addNumber("SizeZ",0);
+		Dialog.addCheckbox("Select PCR file",false);
+		Dialog.show();
+	
+		if (Dialog.getCheckbox()== false) {
+			// Enter manually
+			pcrSizeX = Dialog.getNumber();
+			pcrSizeY = Dialog.getNumber();
+			pcrSizeZ = Dialog.getNumber();
+			
+		} else {
+			
+			// Select new path
+			pcrPath = File.openDialog("Select PCR file to import");
+		}
+	}
+}
+// Import VOL file
+//print(filePath);
+run("Raw...", "open=["+filePath+"] image=[32-bit Real] width="+pcrSizeX+" height="+pcrSizeY+" offset=0 number="+pcrSizeZ+" gap=0 little-endian");
+
+
diff --git a/Import_VOL_Python.py b/Import_VOL_Python.py
new file mode 100644
index 0000000..aa66ea7
--- /dev/null
+++ b/Import_VOL_Python.py
@@ -0,0 +1,37 @@
+import numpy as np
+
+def load_nanotom(path, pcrSizeX = 0, pcrSizeY = 0, pcrSizeZ = 0):
+    
+    if pcrSizeX == 0 or pcrSizeY == 0 or pcrSizeZ == 0:
+        print('searching pcr file for image dimensions')
+    
+        pcrpath = path.split('.')[0]+'.pcr'
+        
+        if not os.path.exists(pcrpath):
+            print('pcr-file not found, please provide image dimensions manually')
+        else:
+            with open(pcrpath) as file:
+                lines = file.readlines()
+                
+            for line in lines:
+                splitline = line.split('=')
+                if splitline[0] == 'Volume_SizeX':
+                    pcrSizeX = int(splitline[1])
+                if splitline[0] == 'Volume_SizeY':
+                    pcrSizeY = int(splitline[1])
+                if splitline[0] == 'Volume_SizeZ':
+                    pcrSizeZ = int(splitline[1])
+                    
+    else:
+        print('dimension manually provided as '+str(pcrSizeX)+'x'+str(pcrSizeY)+'x'+str(pcrSizeY))
+        
+    print('dimensions considered as '+str(pcrSizeX)+'x'+str(pcrSizeY)+'x'+str(pcrSizeY))
+    
+    print('load the file')
+    
+    with open(path,'r') as file:
+        file.seek(0)
+        im = np.fromfile(file, dtype='<f4').reshape(pcrSizeX,pcrSizeY,pcrSizeZ, order ='F')
+        
+    return im    
+    
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