Imspector MSR: NumberFormatException when parsing timepoints

[dgault]

This issue was raised on Imagesc thread https://forum.image.sc/t/msr-files-in-bio-formats/90582 and a sample file was provided at https://zenodo.org/records/10476252?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6IjQ1ODRiNjkwLWExNTUtNGJlZS1hYjJhLTNjOTgzZWRiNmUwZCIsImRhdGEiOnt9LCJyYW5kb20iOiJhZjI1M2JjZDc4Y2Q5ZjE0MzhiMTZhOWQwMWRkYWQ2ZiJ9.Xz8eb6cxS-jWu5GvAnYEqkKlFzjLNoYYc3bI3mjtci7tinEdRZIvj8CjTyHqTNJj1waBVpaNJZvK8IvN0y3Y0g

Using the provided sample file the issue can be reproduced with Bio-Formats 7.1.0

The stack trace for the exception is as below:

java.lang.NumberFormatException: For input string: "2.8E-43"
	at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
	at java.lang.Integer.parseInt(Integer.java:580)
	at java.lang.Integer.parseInt(Integer.java:615)
	at loci.formats.in.ImspectorReader.initFile(ImspectorReader.java:429)
	at loci.formats.FormatReader.setId(FormatReader.java:1480)

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/msr-files-in-bio-formats/90582/6

[scuniff]

I was able to re-produce the issue with the test image in Fiji.

In Eclipse, I modified the code in https://github.com/ome/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ImspectorReader.java

The changes are below.

The variable valueType was 9 during the error so I moved the case 9 statement down to the section that does readInt().
It was doing readFloat() which I think causes the Exception later at line 429 as noted in stack trace in original message.

Line 316:

      switch (valueType) {
         case 10:
         case 11:
         case 12:
             key = value;
             value = String.valueOf(in.readInt() == 1);
             break;         case 2:
         case 3:          
//       case 9:                                    // moved to section below that does readInt() 
         case 13:
         case 14:
         case 17:
             key = value;
             value = String.valueOf(in.readFloat());
             break;
         case 0:
         case 1:
         case 4:
         case 5:
         case 6:
         case 8:
         case 9:                   // added case 9
            key = value;
           value = String.valueOf(in.readInt());
           break;

With the code change the error did go away and I got the Image below.

Not sure if this image is correct

Not sure if this is the right fix.

Not sure what else this might break.

Just thought I'd share this info. :)

[scuniff]

Referring to the original code, "Time Time Resolution" is the value of variable key when the exception occurs at line 429. The exception occurs because it is doing a readInt() but was parsed using readFloat() at line 330. Note the string "2.8E-43" in the stack trace exception.

In Eclipse I made some changes to only have the logic changed for when variable valueType is 9 and key is “Time Time Resolution”.

Starting back from the original version of ImpsectorReader.java, I just added an if statement to do readInt() when key is “Time Time Resolution” for case 9.

      case 2:
      case 3:                 
      case 9:                   
      case 13:
      case 14:
      case 17:
        key = value;
        if (key.equals("Time Time Resolution")) {
            value = String.valueOf(in.readInt());            	
        }
	// This does original logic
        else {
        value = String.valueOf(in.readFloat());
        }
        break;

The results are the same as before.

No exception
Image looks the same as above.

[dgault]

Thanks @scuniff for the testing, if you are happy that solution is working then do you want to open it as a PR and we can test it against our repository of sample files?